WPC , Jxk03|Jx "j$3|`Bi ( WP_TV12910031mswordortsnt0esPs1 WPTVWPC218A[2< WRA3A J8k8 f xh 3xJxmDBi2<&Ma H6and in archiving them for years past when an author may be able to. NqTwo commonly used archives of molecular biology software are IUBio Archive, at Indiana University, andthe European Bioinformatics Institute (EBI) software archive. Internet resource locators (URLs) for theseare $Qq' '$1ͪ  Ы11  1EBI at http://www.ebi.ac.uk/ or ftp://ftp.ebi.ac.uk/0RF' '01ͪ  Ы11  1The European Bioinformatics Institute, home to EMBL databank and others, and a home to a largemolecular biology software archive, including the very useful Bio Catalog of software(http://www.ebi.ac.uk/biocat/biocat.html).$U' '$1ͪ   Ы11   1IUBio at http or ftp://iubio.bio.indiana.edu/0V' '01ͪ   Ы11  1IUBio Archive is home to a large collection of biology software, and also provides services for keywordsearching of current GenBank, SwissProt and PIR databanks, and the useful Bionet network news archive. It has been operating since 1989, as a user- and author- supported self-service archive. The molecularbiology software collection at IUBio is also mirrored (copied) to sites around the world, including theFinland, Sweden, Japan, United Kingdom, France, Spain, and Israel. See the following software listingssection for URLs to these.\fA few of many other Internet servers of note include$]fw' '$1111http://www.ncbi.nlm.nih.gov/ - home site for up-to-date access to Entrez software (databankx' 'lookups), Sequin for publishing your sequence in GenBank, Macaw (multiple alignment), and others.$_x' '$1111http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html - Search Launcher at;' 'Baylor College of Medicine, home to a selection of sequence analysis methods. Recommended is theirsearch launcher program (a Perl script that is usable on Macintosh and Wintel systems) for batch access tothis valuable resource.$ c' '$1111http://expasy.hcuge.ch/ - home of SwissProt, ProSite and home to a collection of useful database' 'analyses functions, especially for protein data.$ e' '$1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq11.3 Fetching software 0 f' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1File Transfer Protocol (FTP) is an Internet service designed specifically for file transfer. It is an antecedent' 'of the popular Hypertext Transport Protocol (HTTP), or web, Internet method. Generally FTP is still abetter method for transferring large files such as software packages, than is a web browser. One popular' 'and easy to use FTP program for MacOS is the Fetch program by Jim Matthews of Dartmouth College. M' 'Find more information at http://www.dartmouth.edu/netsoftware/fetch.html. The ubiquitous Netscape or_' 'other web browser also lets you fetch software either via HTTP or FTP methods. lGenerally software is stored and transferred to you in encoded formats from archives. Most current fetchingsoftware, like Fetch and Netscape, will decode this automatically for you. However, other softwaresometimes is used or needed for decoding. General Internet software packages and servers will get youstarted on what is needed. If in doubt, your local library or bookstore will have a few shelves full of bookson using Internet services and general software archives.  qThe main trick in fetching software these days is knowing where to look. Besides this review, you canmake use of web links made by others, perhaps with better perspective than this author. See also the6 &s H6common Internet search services, like Yahoo (http://www.yahoo.com/), AltaVista(http://www.altavista.digital.com/), Lycos (http://www.lycos.com/) or others.u/Keep in mind that software is updated; if the version you try fails in some way, a newer version may beavailable now or soon. The author's preferred or home server is the best place to check for updates, asarchive servers don't always have the current release.$x/c' '$1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq11.4 Setup and use 0ydydW' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1Once on your computer, the steps of installing and configuring free software range from easy to trying. yl' 'Instructions are usually included, but are not always detailed enough, or cover all the range of problems onecan run into. Special installing software is common with commercial software, but not with the freevariety. }yReport problems you have to the author, and suggestions for improving the software. Asking thefrequently overworked authors for help with installation isn't always good solution though, so attention totheir pre-written installation directions is essential. Special kinds of software, especially those written for Java or Perl, will require that you also fetch andinstall other free, general software to use. In the case of Java, this is becoming less a problem as newMacOS and UNIX systems are shipping with a Java runtime as part of the system.$ '' '$1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq11.5 Multi-platform software 0 ( = (' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1By 1998 counts of Internet browser contacts at IUBio and other biology web servers, from 30% to 50% of =0' 'biologists use Macintosh computers, 40% to 70% use Wintel systems, with somewhat less than 10%using XWindows systems as their workstation (though many use UNIX or VMS for other things). Bioscientists remain diverse in their computing system choices and needs for software. Many use or haveaccess to multiple operating systems, depending on what software runs on. Also of help, there arecommercial emulator programs that allows one to run most MS Windows and MSDOS software onMacintoshes, and conversely to run some Macintosh programs on Wintel systems  = Some software is written to run on many operating systems. This may be a holy grail of those whodevelop scientific applications - one hopes a program can be used by anyone needing it, on any computersystem. It isn't as easy to write multi-platform software as might be. Outside of the recent arrival of Java,there hasn't been an easy, good way to do this inexpensively. Even large commercial developers expendeffort that is not always successful (e.g., WordPerfect on UNIX pales compared to the MacOS or Wintelversions).  With the case of graphical interface software that most of us expect today, multi-platform programs maynot look quite right on your particular system, even though they operate as intended. In the more commoncase of software with no graphical interface, you may need to devote extra time to learning itscommand-line or menu driven syntax.  fThe new Java development system born at Sun Microsystems (http://www.javasoft.com), now is providinga means for developing useful software that works well on common systems, albeit at present Java softwareis frequently slower than its counterpart written in C++, C or other languages. We may expect to see muchmore software in biocomputing written in Java in coming years. See for instance the new sequencing6 & H6analysis package from Licor (www.licor.com).$ f ' '$y1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq11.6 Client-Server biosequence software 0  ' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1There are various developers working on the concept of separating the user interface from the analysis &' 'programs, and I think this is be a useful approach to making such programs easier to use. This is the basisof a client-server design for software. Simple examples of this are web interfaces that abound now forvarious data analyses. $ (' '$This author's own work-in-progress SeqPup takes this approach: it allows you to use the analysis software )l' 'you need, whether Clustal, CAP, tacg, fastDNAml, or others, running on your own computer or on a :~' 'server computer. SeqPup provides a graphical interface and standard user interface methods for editingsequences, basic manipulations and alignments, and sophisticated display and output options. It also linksto analysis "engines" in a way you can configure to your taste. These analysis programs encode thecomplex data analysis algorithms but generally without a user-interface beyond command-line options. With a client program such as SeqPup, use of these programs is simplified and tied into a way for you toorganize your sequence data.$ ) ' '$Martin Senger at EMBL/EBI is working on a general CORBA interface to sequence analysis software called ' 'AppLab (http://industry.ebi.ac.uk/applab/), which is a similar approach.0  ƀ ' '0Peter Rice's EMBOSS (http://www.sanger.ac.uk/Software/EMBOSS/) will be a freely distributable set of ' 'analysis programs, still under development at this writing. It will run on UNIX server computers, with acommand-line interface. EMBOSS will include various sequence analysis topics, and will include a majoreffort to provide easy integration of other public domain packages. Analyses include rapid databasesearching with sequence patterns, and for sequence overlaps, simple and species-specific repeatidentification, nucleotide sequence pattern analysis, codon usage analysis for small genomes, geneidentification tools for genomic sequencing, rapid identification of sequence patterns in large scale sequencesets, protein motif identification, and presentation tools for publication. cThese could be the basic analysis engines for sequence analysis, and some client program with a good userinterface, perhaps like SeqPup, Java applets, or web forms, can be the program you use to run the analyses. $ d ' '${1ͪ    Ы 11    12. Free software highlights0  ʀ' '01ͪ  +Z$$Z$$+  Ы  11      qZ$Hl Dh@dq12.1 Clustal sequence alignment 0   ـ' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1Clustal provides automatic multiple sequence alignment. The current version is called Clustal W, and is ' 'available for MacOS, Wintel, UNIX, and VMS computers. The simultaneous alignment of manynucleotide or amino acid sequences is now an essential tool in molecular biology. Multiple alignments areused to find diagnostic patterns to characterize protein families; to detect or demonstrate homology betweennew sequences and existing families of sequences; to help predict the secondary and tertiary structures of newsequences; to suggest oligonucleotide primers for PCR; as an essential prelude to molecular evolutionaryanalysis. The Clustal program fits this need very well. It is available atftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW and at EBI and IUBio archives. There is a companion programClustalX which provides a graphic interface to Clustal, and Clustal can be used from other sequence editors' 'such as SeqPup.b X G G& X H' 'b1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq12.2 Entrez to search genome data ÿ0 h } h' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1The Entrez program is used for keyword searches of gene sequence data and Medline literature. It has been }' 'written by the programming staff at the National Center for Biotechnology Information (NCBI). It can beobtained from http or ftp://ncbi.nlm.nih.gov/. Entrez runs on a variety of computer systems. One bigadvantage of Entrez is the inclusion of a subset of MEDLINE, which covers the abstracts of entriessubmitted to the sequence databases. The WWW service of NCBI also offers an Entrez type of capabilitythrough your web browser. The program source for Entrez developed at NCBI has been instrumental inproviding a software framework for other biosciences applications, including a version of SeqPup andClustal-X.$ } ' '$1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq12.3 NIH Image for image analysis 0  ' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1A very useful Macintosh program for general image analysis is NIH Image, written by Wayne Rasband. ' 'Image can be used to measure the area, average density, center of gravity, and angle of orientation of a userdefined region of interest. It also performs automated particle analysis and can be used to measure pathlengths and angles. Measurement results can be printed, exported to text files, or copied to the clipboard. Results can be calibrated to provide real world values. Find Image atftp://zippy.nimh.nih.gov/pub/nih-image/, or http://rsb.info.nih.gov/nih-image/. There is now a versionfor MS Windows, from http://www.scioncorp.com/ .$' '$1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq12.4 PHYLIP for phylogeny analyses 00' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1The widely used Phylogeny Inference Package, PHYLIP, from Joseph Felsenstein, is a package ofE' 'programs for inferring phylogenies (evolutionary trees), and written to work on as many different ofcomputer systems as possible. It includes analyses of DNA and protein sequences, restriction sites, distancematrices and gene frequencies, quantitative and discrete characters, and plotting of evolutionary trees. Algorithms used include parsimony, maximum likelihood, neighbor joining and several others. Manyoptions for precise control of the analyses are available. The home for PHYLIP is at http orftp://evolution.genetics.washington.edu/. $(' '$1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq12.5 RasMol for molecular modeling 0(=(' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1RasMol is a widely used, free molecular graphics program for the visualization of proteins, nucleic acids=' 'and small molecules. The program is aimed at display, teaching and generation of publication qualityimages. RasMol runs on all common computer systems. The program reads in molecule co-ordinatesand interactively displays the molecule in a variety of color schemes and molecule representations,including depth-cued wireframes, space-filling spheres, ball and stick, solid and strand biomolecular ribbons,atom labels and dot surfaces. The home for RasMol is ftp://ftp.dcs.ed.ac.uk/pub/rasmol/1 11 1$=' '$1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq12.6 SeqPup for sequence editing 0 >' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1SeqPup, and its predecessor SeqApp, are biological sequence editor and analysis programs. They includesS' 'links to network services and external analysis programs. SeqPup is usable on common computer systems,using the new Java language.  Features include multiple sequence alignment and single sequence editing, read and write several sequence6 % H6file formats, pretty print of alignments and sequences with boxed and shaded regions, sequence featureediting, manipulation and marking in prints, consensus, reverse-complement, distance/similarity, translateDNA to/from protein. Print file formats include PICT, Postscript and GIF.EUser-definable links to external analysis programs, including ClustalW multiple alignment, CAP contigassembly, tacg restriction maps, fastDNAml phylogenetic analysis are included, and others can be added byyou. One can use these running on your own computer or on an Internet server computer, using a newCORBA protocol (www.corba.org). Internet sequence analysis services include fetching sequences usingSRS keyword search, and performing NCBI-BLAST similarity searches.FThe home for SeqPup is http://iubio.bio.indiana.edu/soft/molbio/seqpup/. Note that this application is awork in progress; it has bugs. SeqApp is the Macintosh-only predecessor to SeqPup. Many folks find thiscurrently a more useful program than SeqPup. It is faster, but lacks newer features of SeqPup.$' '$1ͪ    Ы 11    13. Software use issues0' '0|1ͪ  +Z$$Z$$+  Ы  11      qZ$Hl Dh@dq13.1 Copyrighted versus public domain 0π' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1Most free software is copyrighted by the author or sponsor, who retain all rights. They specifically grant' 'you a right to use this software freely, perhaps only for non-commercial uses. Use of copyrighted softwarein commercial packages or other uses that make money require consent from the author. Many of the freesoftware programs come with source code, so you can modify and extend it. This is a great boon to letsophisticated users do a needed analysis, but keep in mind use of such in a commercial product isn'tallowed. If the author explicitly places his work in the public domain, s/he retains no control, and it canbe used in commercial applications. $n' '$1ͪ  +Z$$Z$$+Ы  11    qZ$Hl Dh@dq13.2 Citing software publications 0oo]' '01ͪ  +Z$$Z$$+Ы 11   qZ$Hl Dh@dq1Publicly available software is a publication, and free software that you use should be treated withr' 'consideration that you give other publications used in your research. While some free software has acompanion paper publication to cite, some does not. It is usual practice to cite a software publication withits Internet URL in place of the journal/volume portion, e.g., FZ y ##%%''F1ͪZZyZ  &Z$$y$$&Ы 11 yZ  qy$Hl Dh@dq1Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author at''ftp://evolution.genetics.washington.edu/. Department of Genetics, University of Washington, Seattle. %%Gilbert, D.G., 1996. SeqPup, biosequence editor & analysis platform, version 0.6. Bionet.Software, July1996. See also ftp://iubio.bio.indiana.edu/molbio/seqpup/A y Z ##' 'A1ͪyZZZ &y$$Z$$&Ы 11 ZZ qZ$Hl Dh@dq1Some of these programs have been available at the same location for 10 years or more, so there isn't a' 'general problem of impermanence with Internet locators.$ <' '$1ͪ    Ы 11    14. Acknowledgments0 =L=+' '01ͪ    Ы 11     1The many developers of free software for biosciences, some of them mentioned herein, are the real authorsL:' 'of this document. If you use their software, please let them know you find it useful. Often one programbuilds upon others. This author would like to thank Jonathan Kans, Joseph Felsenstein, Michael Zuker,Gary Olsen, Dan Davison, Rob Harper, Dave Kristofferson, Reinhard Doelz, Rainer Fuchs, PeterMarkiewicz, Thure Etzold, Xiaoqiu Huang, Des Higgins, Harry Mangalam, Jim Brown, Bill Pearson, and6 & L H6many others who provided their sweat and ideas to help make his own works useful. The many users ofsoftware who offer suggestions, criticisms and insights on how software should work, also contributeenormously to making free software better for all to use. The former GenBank home at Intelligenetics inthe 1980s held an archive for free molecular biology software, to which many of us owe thanks for theirpioneer efforts. L 1ͪ  Ы11  1   $-' '$1ͪ    Ы 11    15. Software listings0.=.z' '01ͪ    Ы 11     1This list of over 150 free software programs in molecular biology and related areas is not exhaustive by any=' 'means, but includes much of what is available for Macintosh and/or MS Windows computers. $=_' '$Operating system key: M - MacOS, W - MS Windows or MS DOS, O - Other (Unix usually)0`q`' '0Software archive abbreviations:$q' '$1ͪ0Z$$Zgy$$0Ы11qZgy$Hl Dh@dq1 ebi - ftp://ftp.ebi.ac.uk/pub/software/ or http://www.ebi.ac.uk/software/software.html0π' '0 iubio - ftp://iubio.bio.indiana.edu/molbio/ or http://iubio.bio.indiana.edu/soft/molbio/0 ' '0 Alternate sites for the IUBio molecular biology collection:  ftp://ftp.funet.fi/pub/sci/molbio/iubiomolbio  ftp://ftp.sunet.se/pub/molbio  ftp://ftp.nig.ac.jp/pub/mirror/IUBIO/molbio  ftp://ftp.uam.es/pub/mirror/molbio, ftp://ftp.pasteur.fr/pub/GenSoft/mirrors/IUBio/molbio http, ftp://mic3.hensa.ac.uk/hosts/iubio.bio.indiana.edu/molbio/  ftp://bioinformatics.weizmann.ac.il/pub/software/mac and software/ibmpc  11ͪ0Zgy$$Z$$0Ы11qZ$Hl Dh@dq1Some Email addresses and home URLs may be out of date. Unless otherwise indicated, all software listedis copyrighted by the author, and is available free for non-commercial use. Specific copyright restrictionsshould be noted. Some of this software is shareware, the author requesting a fee for use.#2f$fw $%x' '$ 1ͪ+Z$$Z$$+Ы11qZ$Hl Dh@dq1ABaCUSfM, W, O0&' '01ͪ+Z$$Z$$+Ы11qZ$Hl Dh@dq1ABaCUS is a no-frills program to investigate the significance of the putative correspondence between exonsand units of protein structure.F(Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Arlin Stoltzfus, arlin@is.dal.ca7) %%' '71111Archive:iubio/evolve/abacus/M*π Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ADE-4M0+-' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1ADE-4 is a multivariate analysis and graphical display software package for Macintosh micro-computers.F,Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Olivier J.M. and others, Jean-Michel.Olivier@biomserv.univ-lyon1.fr7-P%%' '71111Home:ftp://biom3.univ-lyon1.fr/pub/mac/ADE/ADE4, http://biomserv.univ-lyon1.fr/ADE-4.htmlM.&b Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Amplify  M0/'8's' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This Macintosh software is for use in designing, analyzing, and simulating experiments involving the6 8&08 H6polymerase chain reaction (PCR). Amplify will search a target sequence for near matches and display theresults of using various primers. It can check oligos for matching sequence and for internal repeats.F28|Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author: Bill Engels, WREngels@macc.wisc.edu73}}#%%' '71111Archive:iubio/mac/amplify*, ebi/mac/M44 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1AnalyzeSignalase U M05F' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A Macintosh program for applying the algorithm of von Heijne to the prediction and analysis ofmammalian signal sequences. It uses a weight- matrix method to try to predict the site at which signalpeptides in secretory peptides are cut off by the signal peptidase.F8Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author: Ned Mantei79%%' '71111Archive:iubio/mac/analyze-signalase*M: Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1AncestorW0;  ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Ancestor is designed to infer ancestral amino acid sequences from a set of homologous amino acid sequenceswhose phylogenetic relationships: ==Z  ##%%:1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1are known. + >=N%%' '+1111Author:Jianzhi Zhang, zhang@imeg.bio.psu.edu7 ?O`O%%' '71111Archive:iubio/ibmpc/ancestor*M @`q` Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1AnnhybW0 Arr' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Annhyb is a little program for Windows 95 that is able to calculate various DNA sequence (degenerated ornot) parameters. FCZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:O. Friard & G. Stefanuto, friard@ba.cnr.it7DL%%' '71111Home:http://area.ba.cnr.it/~e105of01/annhyb221.zip+ME^ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1AntheprotrW, O0Fɀo' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1ANalyze THE PROTeins (ANTHEPROT) is a package includes study of physico-chemical properties:hydrophobicity, antigenicity, flexibility, solvent accessibility, amphiphilicity; secondary structureprediction: Chou & Fasman, Garnier, Gibrat, Deleage, Levin; prediction of transmembranous regions & ofstructural domains; multiple alignment; search for biological sites using PROSITE, and PATMAT; searchfor homologous protein using FASTA; identity level between several sequences. Look and handle proteinstructures from PDB.FLCZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:G. Deleage, deleage@ibcp.fr & C. Geourjon, geourjon@ibcp.fr 7MDUD%%' '71111Home:http, ftp://www.ibcp.fr/7NUfU%%' '71111Archive:iubio/ibmpc/antheprot*MOgxg  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Automatic-BLAST TM0Pxx' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This is an AppleScript that automatically sends sequences by email to the BLAST server atncbi.nlm.nih.gov at prescribed times, daily or weekly. The script uses the scriptable email program Eudora.FRZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Brian Osborne, bosborne@nature.berkeley.edu7SS%%' '71111Home:http://pgebaker4.pw.usda.!gov/bio/bio.html7Td%%' '71111Archive: iubio/mac/automatic-blast.*MUv Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1BCM Search LauncherM, W, O (Perl)bV &V  H' 'b1ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1The BCM Search Launcher is an integrated set of World- Wide Web pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point-of-entryfor related searches. There is a batch client interface for Unix and Macintosh computers that allowsmultiple input sequences to be automatically searched as a background task, with the results returned asindividual HTML documents. Requires Perl.F[ZZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Randall F. Smith et al.7\ZkZW%%' '71111Home:http://gc.bcm.tmc.edu:8088/search-launcher/launcher.htmlM]l}li Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1BufferStackv M0^}}z' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Given the appropriate information, the BufferStack will construct a complete recipe for a buffer that isdefined in terms of both pH and ionic strength, at the temperature of use. F`Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Rob Beynon7a%%' '71111Archive:iubio/mac/buffer*, ebi/mac/bufstack*MbÀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1CabufferW0c' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This program allows you to calculate the concentrations of all ionic species present in a mixture of up tofour divalent cations and four ligands for these ions. Examples of such buffers are EDTA, EGTA, NTA,HEDTA, citrate, Ca-binding proteins, etc. Corrections for temperature, ionic strength and pH are provided. F fZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Jochen Kleinschmidt, kleinschmidt@mcclb0.med.nyu.edu7 g,%%' '71111Archive:iubio/ibmpc/cabuf*M h,=,) Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1CAIC M0 i>O>;' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1CAIC, Comparative Analysis by Independent Contrasts, computes phylogenetically independent contrastsfrom comparative data, allowing valid statistical testing of adaptational hypotheses. The manual givesguidance on testing hypotheses of correlated evolution among traits, rate variation among traits or taxa, andgrade shifts. F mOZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Andy Purvis & Andrew Rambaut, Andrew.Rambaut@zoology.ox.ac.uk7n%%' '71111Home:http://evolve.zps.ox.ac.uk/CAIC/CAIC.htmlMo Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1CAPzM, W, O0p' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Contig Assembly Program based on sensitive detection of fragment overlaps. C source, command-lineprogram, can be used from SeqPup, others.FrZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Xiaoqiu Huang, huang@cs.mtu.edu7s%%' '71111Home:ftp://cs.mtu.edu/pub/huang/7t%%' '71111Archive:iubio/align/cap*Mu!  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1CGRM0v!2!' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A HyperCard stack for presenting nucleotide sequence data using Chaos Game Representation.Fw3DZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Heikki Lehva, lehvaslaiho@cc.helsinki.fi7xDUDA%%' '71111Archive:: iubio/mac/cgr*, ebi/mac/cgr*MyVgVS Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Clustal W_M, W, O0zgxgd' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A multiple sequence alignment program, which is widely used and described in the article Clustal W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting,6 &|  H6position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680(1994).F}yZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Higgins et al.7~%%' '71111Home:ftp://ftp-igbmc.u-strasbg.fr/pub/Clustal*7#%%' '71111Archive:ebi/mac/clustalw*, ebi/dos/clustalw*, iubio/align/clustal*M4 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ClustalXeM, W, O0F' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1ClustalX is a graphic interface for the ClustalW alignment program. The sequence alignment is displayed ina window on the screen, with pull-down menus. F&Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Thompson J.D et al., julie@igbmc.u-strasbg.fr7&7&z%%' '71111Home:ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalXM8I8 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Codon Frequency Analyzer0W0 IZI' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This program helps to identify coding regions of DNA by comparing the codon frequencies in knowncoding regions with a sequence of DNA, the coding regions of which are unknown. The program will workwith any organism.F [Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ballyclaire Analysis7 %%' '71111Archive:iubio/ibmpc/codon*M  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1CodonBiasIndexeM0 ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1The codon bias index is a statistic created by Bennetzen and Hall to quantify the extent to which morefrequently used codons are used in preference to less frequently used codons. FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Tom Ritch, ritch@seas.ucla.edu7;%%' '71111Archive:iubio/mac/codonbioasindex*M L Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ComapW0  ^' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for helping with the construction of,restriction maps of small DNA fragment from digestion data. The program works under a graphical userinterface.F-OZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Kay Hofmann, khofmann@cipvax.biolan.uni-koeln.de7PaP%%' '71111Archive:iubio/ibmpc/codon*, ebi/dos/Mara Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ConsInspectorKM, W, O0ss' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1ConsInspector uses a precompiled library of extended weight matrix descriptions (consensus profiles) oftranscription factor binding sites to scan nucleic acid sequences for matches to these sites.FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:K. Frech, et al. frech@gsf.de7%%' '71111Home:ftp://ariane.gsf.de/pub/M  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1CovariationyM0ʀ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A Hypercard stack for phylogenetic comparative analysis of aligned RNA sequences.FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:James W. Brown, jwbrown@mbio.ncsu.edu7A%%' '71111Archive:iubio/mac/covariation*, ebi/macMS Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1CPrimerM0!d' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1CPrimer evaluates oligonucleotides as possible PCR primers. It shows melting points, interfering' 'structures, and can search for optimum amplification pairs."D3 3& D HZ  ##%%' '1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Greg Bristol, gbristol@ucla.edu7UfU%%' '71111Archive:iubio/mac/cprimer*Mfwf Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DCSE W, O0xx#' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Dedicated Comparative Sequence Editor is a multiple alignment editor. It can be used to edit protein, DNAor RNA alignments. The structure of the molecules can be incorporated in the alignment. It offers lots offeatures such as color display of characters and structure, automatic alignment relative to sequences alreadyaligned with others, sequence grouping, sequence or pattern searching, marker system, checking ofincorporated RNA structure, on-line hypertext help, macros, and a lot more.FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Peter De Rijk, derijkp@reks.uia.ac.be7%%' '71111Home:http://www-rrna.uia.ac.be/~peter/dcse7%%' '71111Archive:ebi/dos/dcseM Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DigestW 0&' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Digest scans DNA sequence files for restriction sites. It prompts the user to specify which enzymes to cutwith, and if they are in the enzyme 'Idatabase, it writes out the positions of all the cuts and sorts the fragments by size.F J[Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ramin Nakisa, ramin@ic.ac.uk7 [l[%%' '71111Archive:iubio/ibmpc/digest*, ebi/dos/digest*M m~m Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DigispeakM0 ~~)' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for reading sequencing gels with the aid of a Graf-Bar or similar sonic digitizer. FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ned Mantei, bcmantei@aeolus.vmsmail.ethz.ch7L%%' '71111Archive:iubio/mac/digispeak*, ebi/mac/M^ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DispanW0Āo' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1DISPAN (genetic DIStance and Phylogenetic ANalysis) is designed to compute the following:average heterozygosity and standard error for each population; gene diversity and associated parameters;standard genetic distances and errors; DA distances between populations. It also constructs phylogenetictrees and does bootstrap tests.FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Tatsuya Ota, imeg@psuvm.psu.edu7-%%' '71111Archive:iubio/ibmpc/dispan*M->-؀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DNA Runs~M0?P?' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1DNA Runs is a program for performing a significance test of the number of runs in DNA sequencepolymorphism and divergence data. FPsZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:John H. McDonald, mcdonald@udel.edu7ss%%' '71111Home:http://udel.edu/~mcdonald/70%%' '71111Archive:iubio/mac/dna-runs*MA Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DNA SliderzM0S' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1DNA Slider is a program for performing a significance test of heterogeneity in the ratio of polymorphicsites to fixed differences in DNA sequence data. FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:John H. McDonald, mcdonald@udel.eduh܀ ܀&  H%%' 'h1111Home:http://udel.edu/~mcdonald/7 %%' '71111Archive:iubio/mac/dna-slider*M    Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DNA StackswM0 ! 2 !#' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1DNA Stacks is a software package of HyperCard stacks providing utilities for viewing and manipulatingmolecular data. DNA Translator includes a gene mapping facility, draws and displays 2 linearized gene mapsfor comparison. Aligner is a stack for editing and display of multiple alignments. Codon Usage displayscodon and amino acid usage data for a variety of organisms and organelles.F 2 xZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. J. Eernisse, DEernisse@fullerton.edu7 x  xz%%' '71111Home:http://biology.fullerton.edu/people/faculty/doug-eernisse7  %%' '71111Archive:iubio/mac/dnastacks*, ebi/mac/M   Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Dna Workbench$M, W, O (Perl)0  ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for sequence searching and manipulation. It offers powerful and fast searches on Genbank andother databases. Client-server access to remote databases and programs. Its many sequence manipulationfunctions include calculating the reverse complement, displaying reading frames and nucleotide to proteintranslations, editing, searching for restriction enzyme sites, searching for human repeat or vector in asequence, comparing a sequence against a library or a user file, searching for a regular expression in asequence. It requires Perl.F  !'Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:James Tisdall, tisdall@cbil.humgen.upenn.edu7 !'!8!')%%' '71111Home:ftp://cbil.humgen.upenn.edu/pub/dnaworkbenchM !9!J!9; Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DNAdraw M0 !J![!JL' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1DNAdraw is a program designed for preparing DNA and protein sequences for publication. A large selectionof highlighting options is available. It has special features for formatting raw data into a style commonlyused for publication, and for doing automatic highlighting of aligned sequences.F !\!Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Marvin Shapiro, mbs@kias.com7!!!%%' '71111Archive:iubio/mac/dnadraw*M!!! Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DNAfragW0!!!' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This program is used in restriction mapping of DNA or sizing of proteins from gels. It calculates the sizeof restriction fragments or peptide bands if standards are run on the same gel, and a standard curve of thestandard bands using their mobilities.F!!Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:John Nash, Nash@biologysx.lan.nrc.ca7!" !%%' '71111Archive:iubio/ibmpc/dnafrag*, ebi/dos/dfrag*M" ""   Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DnaSPW0""-"' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1DnaSP is a package for Windows that performs extensive population genetics analysis on DNA data, forhundreds of sequences of thousands of bases. It estimates several measures of polymorphism within andbetween populations, linkage disequilibrium, recombination, gene flow, gene conversion, and neutrality. DnaSP can do analyses by a sliding window method, and will make graphic representations. F"."sZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Julio Rozas & Ricardo Rozas, julio@porthos.bio.ub.es7"t""tv%%' '71111Home:http://www.bio.ub.es/~julio/DnaSP.htmlh""" "& " H%%' 'h1111Archive:ebi/dos/dnaspM""" Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1DotplotW0"""' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A dotplot program for MS-DOS.F""Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ramin Nakisa, ramin@ic.ac.uk7"""ۀ4%%' '71111Archive:iubio/ibmpc/dotplot*, dprel3*, ebi/dos/dotplot*M"""F Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Dotty PlotterqM0"#"W' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Dotty Plotter is a tool for drawing dot matrix comparisons of sequences in molecular biology. Dot plotsare used to view all areas of homology between two nucleic acid or protein sequences. F##2Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Gilbert, software@bio.indiana.edu7#3#D#3%%' '71111Home:iubio/mac/dottyplot*, ebi/mac/M #D#U#D Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Double DigesterSM, O0 #V#g#V' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This is a program designed to help researchers in molecular biology assemble restriction maps of DNAusing data from double digest experiments.F #g#Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:L. Wright, wright-lawrence@yale.edu7 ###%%' '71111Archive:iubio/restrict-enz/, ebi/mac/M ### Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1dPrimerM0###' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This Macintosh software is for use in calculating Tm values for degenerate primer. F##Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Haoyuan Chen, hchen@bimcore.emory.edu7###Ѐ)%%' '71111Archive:iubio/mac/dprimer*M###; Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1EditViewM0#$#L' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1DNA Sequence Viewer for ABI Sequencer trace data. EditView is a software application that allows you toview and print analyzed sample files containing sequence data from an ABI PRISM Genetic Analyzer. F$$'Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:EditView@perkin-elmer.com7$($9$(%%' '71111Home:ftp://ftp.abd.perkin-elmer.com/pub/public/Sequencing/EditView/EditView1.0.1.sea.hqx7$9$J$9%%' '71111Archive:iubio/mac/editview*M$K$\$K Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1EntrezrM, W, O0$\$m$\' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Entrez is a molecular sequence retrieval system developed at the National Center for BiotechnologyInformation (NCBI). Entrez provides an integrated approach for gaining access to nucleotide and protein sequence information, to the MEDLINE citations in which the sequences were published, and to asequence-associated subset of MEDLINE. F $n$Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:various at NCBI7 $$$ %%' '71111Home:ftp://ncbi.nlm.nih.gov/entrez/M$$$ŀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Enzyme Kinetics`M0$$$0' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Enzyme Kinetics is a Hypercard stack for Macintosh computers. It calculates and plots the biochemicalvalues for the kinetics of enzyme-catalyzed reactions. F$% Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Gilbert, software@bio.indiana.edu7% %% d%%' '71111Archive:iubio/mac/enzymekinetic*, ebi/mac/enzymekin* M%%.%v Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Esee Wb%.%?%. %.&%? H' 'b1ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Eyeball SEquence Editor, for MS DOS.F%P%aZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Eric L. Cabot, cabot@gcg.com7%a%r%a%%' '71111Archive:iubio/ibmpc/esee*M%s%%s# Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1FastAtM, W, O0%%%4' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1The FASTA sequence comparison programs, improved versions of the FASTP program, originallydescribed in Science (Lipman and Pearson, (1985) Science 227:1435-1441)F%%Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Bill Pearson, wrp@virginia.edu7%%%i%%' '71111Home:ftp://ftp.virginia.edu/pub/fasta/7%%%ʀz%%' '71111Archive:iubio/search/fasta*M%%% Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1fastDNAmlZM, W, O0 %%%' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1fastDNAml is a faster version of Joseph Felsenstein's DNAML (part of PHYLIP). Users should consultthe documentation for DNAML before using this program.F  %&!Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Gary J. Olsen et al., gary@phylo.life.uiuc.edu7 !&"&3&"%%' '71111Archive:iubio/evolve/fastdna*M "&3&D&3 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1FoldItM0 #&E&V&E' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1FoldIt (light) is a molecular modelling program to visualize and manipulate proteins. It has an integratedenvironment in which statistical analysis as well 3D observations can be realized on PDB files. It cananalyze proteins up to 1600 residues. It can extract a number of structural features: Ramachandran plots,SS-bond plots, H-bond plots, and statistics on atomic parameters. F'&V&Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Jean-Claude JESIOR, jean-claude.jesior@imag.fr7(&&&L%%' '71111Home:ftp://ftp.imag.fr/pub/TIMC/FoldIt.html7)&&&^%%' '71111Archive:iubio/mac/foldit*, ebi/mac/M*&&&o Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1GCUAM, O0+&&&' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1General Codon Usage Analysis. This program is designed to calculate various parameters that might berelevant in accessing the codon usage patterns of a group of genes. The user can look at codon usage (orany other statistic) in the dataset as a whole or for each gene individually. Features of this program include: Multivariate analyses of codon usage (RSCU) and amino acid patterns. Calculation of codon usagefrequency, RSCU values, amino acid frequency data, base composition; distances between genes; ability toanalyse complete prokaryotic genomes .F1&'KZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:James O. McInerney, J.mcinerney@nhm.ac.uk72'K'\'K%%' '71111Home:ftp://ftp.nhm.ac.uk/pub/gcua/73']'n'] %%' '71111Archive:iubio/mac/gcua*M4'n''n Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1GelM, W05'''0' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1An application to calculate the size of DNA fragment in an agarose gel.F6''Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Jean-Michel Lacroix, lacroix@medac.med.utoronto.ca77'''S%%' '71111Archive:iubio/mac/gel-jml, iubio/ibmpc/gel-jml, ebi/mac/gel-jml, ebi/dos/gel-jmlM8'''d Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1GelW09'''v' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1GEL takes a set of standard DNA fragment sizes and mobilities and predicts the sizes of unknown6 '׀&:' H6fragments, using a least squares fit to the relationship of mobility and fragment length.F;'( Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:John R. Thompson7<( (( %%' '71111Archive:iubio/ibmpc/gel*, ebi/dos/gel/M=((-(# Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Gel Frag SizerkM0>(-(>(-4' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Gel Frag Sizer is a HyperCard stack which calculates restriction fragment sizes from their mobilities. Twomethods for estimating sizes are provided: the local reciprocal method of Elder & Southern or the cubicspline method.FA(?(sZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Gilbert, software@bio.indiana.edu7B(s((sz%%' '71111Home:iubio/mac/gelfragsizer.*7C(((%%' '7 Archive:ebi/mac/MD((( Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Gel ManageruW0 E(((' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Gel Manager is a user friendly program which runs in MS Windows. It includes techniques of imageprocessing along with options for data analysis. It can deal with different kinds of data such as: RFLP,RAMM, RAPD, microsatellites and other fingerprinting techniques. It is useful for studies includinggenetic relationships, taxonomy and classification , epidemiology, etc.F I((Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Carlos Vaquerizo, Joaquin Dopazo, dopazo@samba.cnb.uam.es7 J()(%%' '71111Home:ftp://ftp.cnb.uam.es/software/molbiol/gel_manM K))") Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1GeneDocW0 L)")3)")' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1GeneDoc is a full featured multiple sequence alignment editor and shading utility. It is intended to help youbring your genetics research work to publication with shading, page and font layout features. FN)4)VZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Karl Nicholas, ketchup@cris.com7O)W)h)W^%%' '71111Home:http://www.cris.com/~ketchup/genedoc.shtml7P)h)y)ho%%' '71111Archive:iubio/ibmpc/genedoc*MQ)z))z Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1GeneMasterzW0R)))' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A small gene analysis package that performs searches for sequences, looks for regions of GC richness,translates using a variety of start codons and genetic codes, and restriction analysis.FT))Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Shawn Abigail, ad873@freenet.carleton.ca7U)))%%' '71111Archive:iubio/ibmpc/genemast*MV)))р؀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1GeneTreetM, W0W)))' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1GeneTree is a program for comparing gene and species trees using reconciled trees. The program cancompute the cost of embedding a gene tree within a species tree, visually display the location and numberof gene duplications and losses, and search for optimal species trees.FZ)*(Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Roderic D. M. Page, r.page@bio.gla.ac.uk7[*)*:*)0%%' '71111Home:http://taxonomy.zoology.gla.ac.uk/rod/genetree/M\*:*K*:A Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1GepasiW0]*L*]*LS' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Gepasi is intended for the simulation of the kinetics of systems of chemical and biochemical reactions.Gepasi is able to simulate the steady-state and time course behaviour of reactions in several compartmentsof different volumes. Results can be plotted in 2D and 3D graphs directly from the program. Steady states6 *&`* H6are analysed with metabolic control analysis and linear stability analysis.Fa*]*Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Pedro Mendes, prm@aber.ac.uk7b***%%' '71111Home:http://gepasi.dbs.aber.ac.uk/softw/gepasi.html7c***#%%' '71111Archive:ebi/dos/Md***ր4 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1HDProbeM0e***F' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1HDProbe matches a probe sequence against a set of alleles and tabulates stable and unstable mismatches. HDProbe accepts probe and allele sequences as input, then displays the sequences with respect to theirorientation in a heteroduplex molecule. Fh*+-Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Marvin Shapiro, mbs@pa.net7i+.+?+.%%' '71111Home:iubio/mac/hdprobe.*Mj+?+P+? Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1HelixVuW0 k+Q+b+Q' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1HelixVu illustrates an 80 bp region of DNA as a helix with the sequence listing printed above the helixdiagram. This view is useful to see the spatial relationship between DNA modifications. F m+b+Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Richard Seyler7 n+++%%' '71111Archive:iubio/ibmpc/helixvu*M o+++ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1HyperW0 p+++' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Hyper is a program for the analysis of enzyme kinetic data under MS Windows. Enzyme kinetic data aresubjected to non-linear regression and the results displayed in five standard graphical forms and printed.Fr++Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:J S Eastery, jse@liverpool.ac.uk7s+++;%%' '71111Archive:iubio/ibmpc/hyper*Mt+++L Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1HyperPCRM0u,,,^' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A HyperCard stack that calculates the optimal annealing temp. of a PCR reaction according to thealgorithm of Rychlik.Fw,,4Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Brian Osborne, bosborne@violet.berkeley.edu7x,4,E,4%%' '71111Archive:iubio/mac/hyperpcr*, ebi/mac/My,F,W,F Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Intron AnalyzerfW0z,W,h,W' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1There are basic differences in the base composition of introns from animals and plants, and this programwill examine introns to find regularities. From a given list of introns you can explore by aligning themeither at the 5' or at the 3' end, or study the adjoining exon-parts. The program will build aconsensus-sequence which shows the most frequent base in each position, including a graphic plot.F~,i,Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Michael Liss, LISS@alf1.ngate.uni-regensburg.de7,,, %%' '71111Archive:iubio/ibmpc/intron-analyzer*, ebi/dos/intana*M,,, Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1LalnviewdM, W, O0,,,0' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1LalnView is a graphical program for visualizing local alignments between two sequences. Sequences arerepresented by colored rectangles to give an overall picture of their similarities. It is able to display sequencefeatures (active site, domain, motif, propeptide, etc.) along the alignment. LalnView is a useful tool foranalysing pairwise alignments and for making the link between sequence homology and what is known' 'about its structure or function.,-:-) -)&-: HZ  ##%%' '1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Laurent Duret, duret@dim.hcuge.ch7-K-\-K%%' '71111Home:ftp://expasy.hcuge.ch/pub/lalnviewM-\-m-\ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Lines&KineticsfM0-n--n#' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A graphic way to calculate linear regressions with normal or logarithmic data, the doubling time of amicrobial culture, and the kinetic parameters for an enzyme reaction. F--Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Manuel G. Claros, claros@uma.es7---W%%' '71111Home:http://www.ie.embnet.org/embnet.news/vol5_1/kinetics.html7---i%%' '71111Archive:iubio/mac/lines-kinetics*M---ŀz Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Linkage-1M0---' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1designed to aid the geneticist in the detection and estimation of linkage in segregating progenies.F --Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Karl A. Suiter, ksuiter@acpub.duke.edu7 -. -%%' '71111Home:iubio/mac/linkage1*M . ..  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1LintrW, O0 ....' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1These programs are for testing the molecular clock on a given topology of a phylogenetic tree and makinglinearized trees, using nucleotide or amino acid sequences.F ...QZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Naoko Takezaki, ntakezak@lab.nig.ac.jp7.Q.b.Q%%' '71111Archive:iubio/evolve/lintr/M.c.t.c Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1LoopDLoop6M, W, O (Java)0.t..t)' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1loopDloop is a tool for drawing and editing RNA secondary structures in molecular biology. A MacOSspecific and Java version are available. Mulfold will generate RNA foldings for display by loopDloop. Arelated program, LoopViewer, lacks the editing features but is simpler to use. F..Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Gilbert, software@bio.indiana.edu7...o%%' '71111Home:iubio/loopdloop/7...%%' '71111Archive:ebi/mac/loop*M...݀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MACAWuM, W0./.' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Multiple Alignment Construction & Analysis Workbench (MACAW) is a program for locating, analyzing,and editing blocks of localized sequence similarity among multiple sequences and linking them into amultiple alignment. It includes sequence alignment search, editing and display. It is a very nice programaccording to many, allowing one to look for blocks of homology in sequences.F//FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Greg Schuler & Stephen Altschul, schuler@ncbi.nlm.nih.gov7/F/W/F%%' '71111Home:ftp://ncbi.nlm.nih.gov/pub/macaw/7/X/i/X %%' '71111Archive:iubio/ncbi/macaw/, ebi/dos/macaw*M/i/z/i Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MacBoxshadebM, O0/{//{0' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for creating good-looking printouts from multiple aligned protein or DNA sequences. Theprogram does no alignment by itself, it uses files from a multiple alignment program. Output can bePostScript, EPSF, PICT, RTF or ASCII text. Identical and similar residues in the multiple-alignment arerepresented by different colors or shadings. There are many options of shading, sequence numbering,' 'consensus output and so on. ///Ҁ /Ҁ&/ HZ  ##%%' '1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Michael D. Baron, michael.baron@bbsrc.ac.uk (macos), Kay Hofmann (original)7/0/%%' '71111Home:ftp://ulrec3.unil.ch/pub/boxshade/macboxshade7000%%' '71111Archive:iubio/mac/macboxshade*M00(0# Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MacPattern|M00(090(4' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1MacPattern is a Macintosh application for protein pattern searches (using PROSITE) and block profilesearches (using BLOCKS). MacPattern assists in finding putative functions for new protein sequences bysupporting pattern searches using the PROSITE database, block searches using the BLOCKS database, andstatistical analyses (maximal segment score analysis and Eguchi-Seto method). F0:0Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Rainer Fuchs, rainer_fuchs@glaxo.com7000%%' '71111Archive:iubio/mac/macpattern*, ebi/macM000 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MacPlasmapvM0000' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1If your study or research involves preparation of circular plasmid maps, you will find MacPlasmap anindispensable tool to have. It draws, stores, and prints high-quality circular plasmid maps with the datayou specify. F 00Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Jingdong Liu7 000%%' '71111Archive:iubio/mac/macplasmap*, ebi/mac/M 01 0 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MacProtM0 1 11 ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1MacProt is a of a set of programs for analyzing protein sequences for secondary structure, chain flexibility,hydropathy, helical wheels, and so on. F 11@Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Peter Markiewicz71@1Q1@L%%' '71111Archive:iubio/mac/plota/, ebi/mac/plota_*M1R1c1R^ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MacStripeM01c1t1co' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1MacStripe is a program for the prediction and analysis of potential coiled-coil regions in protein sequences. MacStripe is the ideal tool for anyone who wants to explore potential alpha-helical coiled coils in thesequence of their protein. With a full Macintosh interface, the results of analyses (raw data or publicationquality plots) can easily be exported to other software. MacStripe uses the algorithm of Andrei Lupas'sCOILS2 for detailed and reliable coiled-coil predictions. F1u1Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Alex Knight, aek4@york.ac.uk7111̀؀%%' '71111Home:http://www.york.ac.uk/depts/biol/units/coils/coilcoil.html7111%%' '71111Archive:iubio/mac/macstripe*M121 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MacTM0222 ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1MacT is a set of programs for the Macintosh to construct and evaluate unrooted trees derived from aminoacid sequences using a distance matrix method.F225Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Angela Luettke & Rainer Fuchs7252F25A%%' '71111Archive:ebi/mac/mact_*, iubio/mac/mact.*M2G2X2GS Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Map Manager_M, W02X2i2Xd' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Map Manager is a program which helps analyze the results of genetic mapping experiments usingintercrosses with codominant markers, backcrosses or recombinant inbred strains in experimental plants or6 2{&2i H6animals. It is a specialized database program which allows easy storage, retrieval, and display ofinformation from such mapping experiments, and it also has tools for searching and for statistical analysisof the experimental results. These tools assist the user in determining linkage among loci and indetermining the order of loci. F2j2Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Kenneth F. Manly, kmanly@mcbio.med.buffalo.edu7222F%%' '71111Home:http,ftp://mcbio.med.buffalo.edu/7232W%%' '71111Archive:iubio/mac/map-manager*, ebi/mac/mapmanager*M333i Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MapMaker^M, W, O033(3z' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1MapMaker is a linkage analysis package designed to help construct primary linkage maps of markerssegregating in experimental crosses. One version performs full multipoint linkage analysis for dominant,recessive, and co- dominant (e.g. RFLP-like) markers.F3)3]Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Whitehead Inst. for Biomedi. Res., mapmaker@genome.wi.mit.edu73]3n3]%%' '71111Home:ftp://genome.wi.mit.edu/distribution/mapmaker373o33o%%' '71111Archive:iubio/mapmaker/M 333 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Materials & MethodsKM0 333' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A Hypercard stack for the storage & retrieval of laboratory procedures. The stack comes pre-loaded withmany commonly-used procedures used in molecular biology.F 33Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:James W. Brown, jwbrown@mbio.ncsu.edu7 333ƀ)%%' '71111Archive:iubio/mac/mandm*, ebi/mac/matmeth*M 333; Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MatildaW0333L' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Matilda is a specialized DNA database management system that helps scientists extract the high-levelinformation that they need for recombinant DNA experiments from a large sequence and genetic informationdatabase. It incorporates functional data and restriction map data. Sequence and functional data are extractedfrom sequence files and from additional information. As recombinant DNA clones are constructed, theirdescriptions are added to the database so that they can be used to describe clones constructed later.F34RZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Isralewitz, B. & Shalloway, D.74R4c4R%%' '71111Archive:iubio/ibmpc/matilda*M4d4u4d Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MatInspectorQM, W, O04u44u؀' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1MatInd is a simple but powerful method to derive a matrix description of a consensus from a number ofshort sequences on which the definition of an IUPAC code would be based. MatInspector is a programthat uses a large library of predefined matrix descriptions of transcription factor binding sites to locatematches in nucleotide sequences of unlimited length. It assigns a quality rating to matches and thus allows aquality- based filtering and selection of matches.F44Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:K.Quandt, et al, quandt@gsf.de7444ހA%%' '71111Home:ftp://ariane.gsf.de/pub/7454S%%' '71111Archive:ebi/mac/matind*, ebi/dos/matind*M555d Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Memsat}W, O055$5v' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1MEMbrane protein Structure And Topology.5$555$ 5$&55 HZ  ##%%' '1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:David T. Jones, jones@bsm.bioc.ucl.ac.uk75F5W5F%%' '71111Home:ftp://ftp.biochem.ucl.ac.uk/pub/MEMSATM5W5h5W Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MetreeW05i5z5i#' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A package for inferring and testing minimum evolution trees. This package is intended to find theminimum evolution tree that has the smallest value of the sum of branch lengths for a set of sequences,identify a set of trees that are not significantly different from the ME tree, and print the trees in apublishable form. F5z5Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Andrey Rzhetsky and Masatoshi Nei, aur1@psuvm.psu.edu7555z%%' '71111Archive:iubio/ibmpc/metree*M555 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MitoProtvM, O0555' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1It supplies a series of parameters that permit theoretical evaluation on mitochondrial targeting sequencesand the importability. MitoProt II provides the possibility to predict mitochondrial proteins harboringtargeting sequences. Chloroplast proteins also can be studied.F56)Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Manuel G. Claros, claros@uma.es, Pierre Vincens 7 6)6:6)%%' '71111Home:ftp://ftp.ens.fr/pub/molbio/, ftp://ftp.rediris.es/software/incoming/science/7 6;6L6;%%' '71111Archive:iubio/mac/mitprot*, ebi/mac/ M 6L6]6L Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1MolwtW0  6^6o6^' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This program calculates molecular weight from an entered chemical formula, and gives concentrations invarious units in response to an entered formula and concentration. F  6o6Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:John A. Kiernan, jkiernan@julian.uwo.ca7 666L%%' '71111Archive:iubio/ibmpc/molwt*, ebi/dos/molwt*M 666^ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Mufold (Mac)pM0666o' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A MacOS port of Michael Zucker's MFold software for prediction of RNA secondary structure by freeenergy minimization, including sub optimal folding with temperature dependence. See also PCFold.F66Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Gilbert (mac port), M. Zuker (MFold)7666%%' '71111Home:iubio/mac/mulfold*, ftp://snark.wustl.edu/pub/ (MFold)767 6%%' '71111Archive:ebi/mac/M7 77  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1NIH Image~M077/7؀' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Image can be used to measure the area, average density, center of gravity, and angle of orientation of a userdefined region of interest. It also performs automated particle analysis and can be used to measure pathlengths and angles. F707dZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Wayne Rasband77d7u7d%%' '71111Home:ftp://zippy.nimh.nih.gov/pub/nih-image/, http://rsb.info.nih.gov/nih-image/M7v77v0 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1NJbafdW, O0777A' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1These programs are for constructing a neighbor-joining or UPGMA tree from allele frequencies ofmicrosatellite DNA or other genetic markers, and computing heterozygosities and Gst.F77Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Naoko Takezaki, ntakezak@lab.nig.ac.jp7777v%%' '71111Archive:iubio/evolve/njbafd/~777̀ 7̀&7 H Z ##' '~1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1NJPlotoM, W, Oÿ0787' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1NJPlot is a phylogenetic tree drawing program that handles files describing trees by the nested parenthesesmethod (e.g. PHYLIP-built trees). Features: A graphical interface allows to re-root a tree anywhere and toswap branches. Bootstrap values are displayed next to internal branches. Branch lengths can be optionallydisplayed. Tree plots can be saved to a PostScript or PICT file.F#88FZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Manolo Gouy, mgouy@biomserv.univ-lyon1.fr7$8F8W8FW%%' '71111Home:ftp://biom3.univ-lyon1.fr/pub/mol_phylogeny/njplot7%8X8i8Xi%%' '71111archive:ebi/mac/M&8i8z8iz Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1NoncodeW0'8{88{' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program that will read an ESEE file containing nucleic acid sequences and produce a distance matrix usingthe Kimura 2-parameter model.F)88Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Eric L. Cabot, cabot@gcg.com7*888%%' '71111Archive:iubio/ibmpc/noncode*M +888 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1NumcloneW0 ,888Ҁ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Estimates the number of clones one has to screen from a genomic library in order to find a desired clone.F -88Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:John Nash, Nash@biologysx.lan.nrc.ca7 .898%%' '71111Archive:iubio/ibmpc/numclone*M /999 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1OligobaseW0099)9)' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This is a shareware program for Windows designed to organize and catalog oligonucleotides collection of abiological laboratory. It stores information about oligonucleotides, select subsets according to specifiedcriteria, print out order forms, calculate molecular weight and melting temperature, and manipulateoligonucleotides.F49*9oZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Igor Sidorenkov, sidorenk@rocketmail.com759p99p%%' '71111Home:http://lochfort.com/oligobase76999%%' '71111Archive:iubio/ibmpc/obase*M7999 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1OligoCRM08999' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1OligoCR is a data management tool for organizing and cataloging oligonucleotide collection. It allows youto store information about the oligos, e.g., the category (PCR, sequencing), type of project the oligo isused for, its application, its description. To search your oligo database, just click the mouse. It has thecapability to proofread your sequences.F<99Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Yongming Sun, ysun@hdklab.wustl.edu7=9: 9 %%' '71111Home:http://hdklab.wustl.edu/~ysun7>: :: %%' '71111Archive:iubio/mac/oligocr*M?::0:0 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1OligoMutantMakerVW0@:0:A:0A' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1OligoMutantMaker simplifies the designing and screening of oligonucleotide-directed single amino acidsubstitution experiments by searching for nucleotide sequences which introduce a restriction endonucleaserecognition sequence into the codon substitution site of the mutant.FC:B:vZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Kevin Beadles et al.hD:v::v :v&D: H%%' 'h1111Archive:iubio/ibmpc/oligo*, ebi/dos/oligo*ME::: Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1OnixW0F:::' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for MS Windows, Onix allows users to examine proteins with known 3D structure from PDB.This program was designed for structure investigation of ligand binding site in proteins. ONIX isinteractive software with a high-performance interface, fast 3D molecular graphics and analysis ofwater-accessible surface. FJ:;Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:A.S.Ivanov et al., ivanov@ibmh.msk.su7K;;;i%%' '71111Home:ftp://org.chem.msu.su/pub/software/Onix/ML;;#;z Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1P1 ClonesM0M;$;5;$' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This is a simple HyperCard stack for keeping track of clones that were constructed with the bacteriophageP1 cloning system. FO;5;XZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ken Abremski, sabremske@esvax.dnet.dupont.com7P;X;i;X%%' '71111Archive:iubio/mac/p1clones*M Q;j;{;j Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1PAMLqM, W, O0 R;{;;{' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Phylogentic Analysis by Maximum Likelihood contains three main programs for model fitting andphylogenetic tree reconstruction using nucleotide or amino-acid sequence data.F T;;Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ziheng Yang, z.yang@ucl.ac.uk7 U;;;%%' '71111Home:ftp://abacus.gene.ucl.ac.uk/pub/paml7 V;;;)%%' '71111Archive:iubio/evolve/paml*MW;;;; Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1PcFoldW0X;;;L' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A PC version of Michael Zuker's RNA-folding program which uses an energy minimization algorithm topredict stem and loop regions of RNA structures. See also MulFold, and home site for Unix versions.FZ;<Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Michael Zuker et al., zuker@snark.wustl.edu7[<<*<%%' '71111Home:ftp://snark.wustl.edu/pub/7\<*<;<*%%' '71111Archive:iubio/ibmpc/pcfold*, ebi/dos/pcfoldM]<<%%' '+1111Home:http://www.uku.fi/~kiviraum/plasmid/plasmid.html7w>>$>%%' '71111Archive:iubio/ibmpc/plasmid-processor*, ebi/dos/plasmidM x>$>5>$ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Plasmid-MakerjM0 y>6>G>6' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Draws linear and circular plasmid maps, allows borders of various widths and fills of grays, arrows, andother options.F {>G>jZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Home:http://yeamob.pci.chemie.uni-tuebingen.de/Archiv/PlasmidMaker.html7 |>j>{>j)%%' '71111Archive:iubio/mac/plasmid-maker*7 }>|>>|;%%' '71111Author:Kai-Uwe Froehlich, kaifr@uni-tuebingen.deM~>>>L Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Primer DesignlW0>>>^' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1PrimerDesign is a DOS program to choose primer for PCR or oligonucleotide probes. It is tailored to checkknown sequences for repeats and unique sequences and subsequently to create primers according to this data.A lot of constrains are available to meet your conditions. It can handle up to 31500 base pairs. Additionalfeatures: unique sequences, repeats, restriction sites.F>>Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Andreas Becker, Joerg Napiwotzki, becker@ps1515.chemie.uni-marburg.de7>?>%%' '71111Home:ftp://ftp.chemie.uni-marburg.de/pub/PrimerDesignM??? Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Primer lM, W, O0??*?؀' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Primer is a computer program for automatically selecting PCR primers. It tests oligos for annealingtemperature, complementarity to genomic repeat sequences, ability to form primer-dimer, and other criteria. Primer annealing temperature calculation is based on thermodynamic parameters. F?+?_Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Steve Lincoln et al., primer@genome.wi.edu7?_?p?_%%' '71111Home:ftp://genome.wi.mit.edu/pub/software/Primer2.27?q??q0%%' '71111Archive: iubio/primer/primer-wi*M???A Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Primer-MastermW0???S' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Automatically search and selection of optimal primers and primers pairs for various variants of PCR;analysis of oligs supposed to be used as PCR primers or hybridization probes; editor for comfortable' 'typing-in new nucleotide sequences;???Ȁ ?Ȁ&? HZ  ##%%' '1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Proutski Vitali, Sokur Oleg, proutski@influenza.spb.su7???%%' '71111Archive:ebi/dosM?@ ? Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Primers! M0@ @@ #' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Primers! is a primer design shareware application, written by the author of Whitehead Institute Primer2. Itallows users to interactively scroll through lists of forward and reverse primers to pick exactly the primerpair wanted. F@@RZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Richard Resnick, rjr@applepi.com7@S@d@Si%%' '71111Home: http://www.applepi.com/7@d@u@dz%%' '71111Archive: iubio/mac/primers*M@v@@v Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ProAnalW0@@@' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1ProAnal is for analysis of multiple protein alignments, studying the structure-function andstructure-activity relationships in protein/peptide families. The program uses aligned amino acid sequenceswith data of their activity and searches for correlations between data on activity and variousphysico-chemical characteristics of different regions in primary structures. F @@Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Alexey Eroshkin, eroshkin@vector.nsk.su7 @@@%%' '71111Archive:iubio/ibmpc/proanal*, ebi/dos/M @A@ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ProAnalyst|W0 AAA' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1ProAnalyst is for investigation of structural differences between proteins divided by functional, evolutionaryor other criteria; structure-activity relationships investigation; searching motifs; protein-engineeringexperiments; and many other protein analysis functions.F AAGZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Vladimir Ivanisenko, Alexey Eroshkin, eroshkin@vector.nsk.su7AHAYAH^%%' '71111Archive:iubio/ibmpc/panalyst*, ebi/dos/proanalystMAYAjAYo Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ProAnWinW0AkA|Ak' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Multiple sequence alignment, analysis of protein sequences and structures, structure-activity relationships,design of protein-engineering experiments. Threads multiple alignment onto known 3-dimensionalstructure; searches linear, spatial sites, conservative and variable in changes of specified physico-chemicalproperties; plots of different physico-chemical profiles for individual or a set of protein sequences; and manyother functions.FA|AZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:I.Pika et al., eroshkin@vector.nsk.su7AAA%%' '71111Archive:iubio/ibmpc/paw*, ebi/dos/proanwinMAAA Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ProfileGraphtW0ABA ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A graphical protein analysis tool.FBBZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Kay Oliver Hofmann, khofmann@biomed.biolan.uni-koeln.de7BB+B0%%' '71111Archive:iubio/ibmpc/prograph*, ebi/dos/pgraph*MB+B<B+A Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1PromFindW0B=BNB=S' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1PromFind is a DOS program that accepts a DNA sequence, and adds a feature table to annotate the locationof putative promoter regions. FBNBqZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Gordon B. Hutchinson, hutch@netshop.bc.cahBqBBq Bq&B H%%' 'h1111Archive:iubio/ibmpc/promfind*MBBB Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ProMSEDW0BBB' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1ProMSED, a Windows application for both automatic and manual DNA and protein sequence alignment,editing, comparison and analysis. Automatic alignment is based on ClustulV; manual alignment and visualanalysis are facilitated by group and block operations and amino acid coloring reflecting their similarity.FBBZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Anatoly Frolov, Alexey Eroshkin, eroshkin@vector.nsk.su7BBBW%%' '71111Archive:iubio/ibmpc/promsed*, ebi/dos/promsed/MBC Bi Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Prophet}W, O0C CC z' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Prophet offers advanced, easy-to-use software tools for data management and visualization, and statisticalanalysis - from simple descriptive statistics to multi-factor ANOVA, logistic regression, and non-linearmodeling. It also offers tools for analyzing biological sequences, including multiple sequence alignment,translation, restriction enzyme and proteolytic cleavage analyses, PCR primer design, BLAST searches,remote database retrievals, and more. FCCvZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Prophet software group, BBN, prophet-info@bbn.com7CvCCv%%' '71111Home:http://www-prophet.bbn.com/M CCC Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Protein Sequence Analysis0W0 CCC' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1The program is a sequence editor with the capability to amino acid composition, hydrodynamic calculation,mass for various isotope labeling, isoelectric point, UV spectrum, relative hydrophobicity, secondarystructure prediction, and others.F CCZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Archive:iubio/ibmpc/prot-sa*M CCC߀L Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1PuzzleqM, W, O0 CDC^' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Puzzle is a maximum likelihood analysis for nucleotide, amino acid, and two-state data. It reconstructsphylogenetic trees from molecular sequence data, and has a fast tree search that allows analysis of large datasets. Puzzle is PHYLIP compatible.FDD6Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Korbinian Strimmer, Arndt von Haeseler, strimmer@zi.biologie.uni-muenchen.de7D7DHD7%%' '71111Home:ftp://fx.zi.biologie.uni-muenchen.de/pub/puzzle7DHDYDH%%' '71111Archive:iubio/evolve/puzzle/, ebi/mac/puzzle, dos/puzzle, unix/puzzleMDZDkDZ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RAMHAW0DkD|Dk؀' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Monte Carlo simulation of the random mutagenesis of synthetic cDNAs.FD}DZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:David P. Siderovski, Siderovski@Galen.OCI.UToronto.CA7DDD%%' '71111Archive:iubio/ibmpc/ramha*MDDD  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RasMolkM, W, O0DDD' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1RasMol is a molecular modelling program for the visualization of proteins and nucleic acids. It readsprotein databank (PDB) files and interactively renders them in a variety of formats, including wire, stick,stick_and_ball, CPK, and ribbon.FDDZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:R. Sayle, ros@dcs.ed.ac.uk7DEDd%%' '71111Home:ftp://ftp.dcs.ed.ac.uk/pub/rasmol/7E EE v%%' '71111Archive:ftp://kekule.osc.edu/pub/chemistry/software/X-WINDOWS/rasmol*, ebi/mac/rasmol*,NE E&E= H' 'Nsoftware/dos/raswin*, AEEM Z ##' 'A1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RbindingW0EME^EM' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Calculates the number of binding sites and the affinities of cell surface receptors for ligands (Scatchardanalysis).FE_EZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Nico van Belzen & Joop van Zoelen, belzen@pa1.fgg.eur.nl7EEEF%%' '71111Archive:iubio/ibmpc/rbindin*MEEEW Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ReadSeqiM, W, O0EEEi' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for converting among several biosequence file formats.FEEZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Don Gilbert, software@bio.indiana.edu7EEE%%' '71111Home:iubio/readseq/7 EEEـ%%' '71111Archive:ebi/mac/readseq*M EEE Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ReAlignW0 EF E' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program that realigns a DNA alignment according to a peptide alignment, thereby improving thealignment in areas not too well conserved.F FF0Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Rasmus Wernersson, RWer@novo.dk7 F1FBF1%%' '71111Archive:iubio/ibmpc/realign*MFBFSFB Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RepFindW0FTFeFT' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1RepFind (promoter find) is a MS DOS program to identify common repetitive elements in DNA sequence.It is also able to identify and mask vector sequence.FFeFZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Gordon B. Hutchinson, hutch@netshop.bc.ca7FFFL%%' '71111Archive:iubio/ibmpc/repfind*, ebi/dos/repfind*MFFF^ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RestdataW0FFFo' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Restriction data and phylogenetic analysis, computes the numbers of nucleotide substitutions per site forpairs of DNA sequences; constructs phylogenetic trees by using the neighbor-joining method.FFFZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Tatsuya Ota, imeg@psuvm.psu.edu7FFF%%' '71111Archive:iubio/ibmpc/restdata*MFGF Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RestSiteW0GGG' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Several programs for analyzing restriction site or fragment data for use in molecular systematics studies.FGG%Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Joyce C. Miller7G&G7G&%%' '71111Archive:iubio/ibmpc/restsite*MG7GHG7 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RNA DotplotqM0GIGZGI ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1RNA Dotplot is a simple utility to print a dot matrix of the potential base pairing interactions in an RNAsequence. FGZG}Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:David S. McPheeters, mcpheeters@biochemistry.cwru.edu7G}GG}A%%' '71111Archive:iubio/mac/rna-dotplot*MGGGS Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RnadrawW0GGGd' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Rnadraw offers RNA optimal structure / basepair-probability matrix / heat curve calculation on Intelcomputers, providing a consistent user interface with many possibilities to view, print, import/export and6 GÀ&G H6edit calculation results.FGGZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ole Matzura, ole@mango.mef.ki.se7GHG%%' '71111Home:ftp://broccoli.mfn.ki.se/pub/rnadrawMHHH# Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1RNA_d2W0HH*H4' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1RNA_d2 is a user-friendly program developed for interactively generating aesthetic and non-overlappingdrawings of RNA secondary structures. It allows easy untangling and editing of RNA molecules > 1000nucleotides long.F H+H_Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:J. Perochon-Dorisse et al., rnad2@ibcg.biotoul.fr7 H_HpH_z%%' '71111Home:ftp://hpsrv.biotoul.fr/rnaM HqHHq Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Sagittarius DnafW0 HHH' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A package for exon/intron structure revealing on the base of protein k-tuples statistic.F  HHZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Victor B. Strelets, strelets@bio.indiana.edu7 HHH%%' '71111Archive:iubio/ibmpc/sag-exo*, ebi/dos/sag-exoM HHH Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Sagittarius PirjW0 HHHȀ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A highly compact databank variant of original PIR database designed to assist individuals in utilization ofsequence database information without huge storage space requests. Includes fast homology searches andselection of sequences by fields (name, source, keyword, etc.), or (non)perfect homology with user-definedshort sequence.F HIZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Victor B. Strelets, strelets@bio.indiana.edu7I I1I ;%%' '71111Archive:iubio/ibmpc/sag-pir*MI1IBI1L Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Sagittarius SeqanalrefGW0ICITIC^' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A dialog shell for storage and manipulation of reference information. This particular variant is oriented onSEQANALREF databases compiled by A.Bairoch.FITIwZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Victor B. Strelets, strelets@bio.indiana.edu7IwIIw%%' '71111Archive:iubio/ibmpc/seqanalr*, ebi/dos/sag-sar*MIII Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SendW0III' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for computing the standard errors of nucleotide diversity and divergence using the algorithm ofNei and Jin.FIIZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Li Jin7III%%' '71111Archive:iubio/ibmpc/send*M III Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SendbsW, O0!IJI ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program that computes average nucleotide substitutions within and between populations using thealgorithm of Nei and Jin. It computes standard errors with a bootstrap method that differs from Nei andJin's.F$JJ7Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Naoko Takezaki, ntakezak@lab.nig.ac.jp7%J8JIJ8S%%' '71111Archive:iubio/evolve/sendbs*M&JIJZJId Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Seq-Eudora-Blast`M0'J[JlJ[v' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Macintosh AppleScript applications that automate your BLAST searches. Drag-and-dropped sequence files6 Jl&(J H6to the BLAST server at ncbi.nlm.nih.gov using Eudora mail. F)JlJZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Brian Osborne, bosborne@nature.berkeley.edu7*JJJ%%' '71111Home:http://pgebaker4.pw.usda.gov/bio/bio.html7+JJJ#%%' '71111Archive:: iubio/mac/seq-eudora-blast*M,JJJ€4 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Seqaid IIW0-JJJF' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Seqaid II is a MS-DOS program for DNA and protein sequence analysis. Functions include editing,modified Needleman-Wunsch alignment, dot matrix comparison, fragment sizer, base composition,translations, protein structure and hydropathicity, restriction site search, and locating potential exons bycodon bias. F1JK+Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Donald Roufa & D.D. Rhoads72K+K<K+%%' '71111Archive:iubio/ibmpc/sequaid*, ebi/dos/sqaid*M3K=KNK= Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SeqAppM0 4KNK_KN' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A Macintosh biosequence editor, analyzer, and network handyman. See SeqPup.F 5K`KqZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Gilbert, seqapp@bio.indiana.edu7 6KqKKq%%' '71111Home:iubio/seqapp/M 7KKK Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SeqPupHM, W, O (Java) 0 8KKK' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1The successor to SeqApp, SeqPup is a biological sequence editor and analysis program. It includes links tonetwork services and external analysis programs. Features include multiple sequence alignment and editing,support for several file formats, sequence feature editing, manipulation and marking, translate dna/protein,consensus, reverse/complement, and distance methods, pretty print of alignments and sequences with boxedand shaded regions, Internet searches, use of external analysis programs, including ClustalW multiplealignment, CAP contig assembly, tacg restriction map, and a remote client-server interface. The currentversion runs on any os supporting Java, an older version runs on MacOS, MSWin and some Unix.F?KL Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Gilbert, seqpup@bio.indiana.edu7@L L1L %%' '71111Home:iubio/seqpup/MAL2LCL2 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SeqSimPresenteraM0BLCLTLC' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1SeqSimPresenter converts a set of aligned sequences to shaded bars of which correspond to the degree ofsimilarity. It presents large alignments in a compact form and allows a fast recognition of the amount,extension, and distribution of conserved regions. FELULZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:cbkfr01@mailserv.zdv.uni-tuebingen.de7FLLL%%' '71111Archive:iubio/mac/seqsimpresent*, ebi/mac/MGLLL  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SequinpM, W, O0HLLL' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Sequin is a stand-alone software tool developed by the NCBI for submitting entries to the GenBank, EMBL,or DDBJ sequence databases. It is capable of handling simple submissions which contain a single shortmRNA sequence, and complex submissions containing long sequences, multiple annotations, segmentedsets of DNA, or phylogenetic and population studies.FLLMZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Jonathan Kans, Colombe Chappey, info@ncbi.nlm.nih.gov7MMMMv%%' '71111Home:ftp://ncbi.nlm.nih.gov/sequin/, http://www.ncbi.nlm.nih.gov/Sequin~NMM&M M&NM& H Z ##' '~1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SeqVuMÿ0OM7MHM7' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1An alignment editor with analysis options that allows you to work quickly and simply with multiplesequences. It is ideal for manually correcting alignments produced using software such as ClustalV.FQMHMkZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:James Gardner, j.gardner@garvan.unsw.edu.au7RMkM|Mk4%%' '71111Home:ftp://gimr.garvan.unsw.edu.au/pub/7SM}MM}F%%' '71111Archive:iubio/mac/seqvu*MTMMMW Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ShmW, O0UMMMi' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Shm was designed to provide assistance in the analysis of somatic (point) mutations induced in theimmunoglobulin genes of B-lymphocytes. It builds clonal trees by parsimony and displays them alongwith somatic mutations.FXMMZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Laurentiu COCEA, cocea@necker.fr7YMMM%%' '71111Archive:iubio/ibmpc/shm*M ZMNM Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SigmaM, O0 [N NN ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1System for Integrated Genome Map Assembly graphical genome map editor. As a viewer, Sigma puts fullcolor maps of the genome in the users hands to display, browse, manipulate, and print. It is capable ofgiving the user a perspective on an entire chromosome map, as well as an arbitrarily detailed view. Features allow the user to find specific parts of a map. Sigma allows the user to integrate data from avariety of sources. A convenient user interface makes data entry easy.F `NNqZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Theoretical Biology and Biophysics Group at LANL, sigma@ncgr.org7 aNrNNr;%%' '71111Home:http://www.ncgr.org/sigma/home.html7 bNNNL%%' '71111Archive:ebi/linkage_and_mapping/SIGMAMcNNN^ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SilmutW0dNNNo' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Silmut helps you to identify regions in a sequence which can be altered to introduce restriction enzyme sitesand other sequences by silent mutations.FfNNZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Raj Shankarappa, bsh@med.pitt.edu, K. Vijayananda, vijay@litsun.epfl.ch7gNNN%%' '71111Archive:iubio/ibmpc/silmut*MhNNN Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Sim2wM, W, O0iNON' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This program build local alignments of two sequences, each of which may be hundreds of kilobases long.FjOO Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Chao K-M et al., zjing@sunset.nlm.nih.gov7kO!O2O!%%' '71111Home:ftp://ncbi.nlm.nih.gov/pub/sim2MlO2OCO2 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SitesxM, W, O0mODOUOD ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Sites is a program for the analysis of comparative DNA sequences. It is primarily intended for data withmultiple closely related sequences. FoOUOxZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author: Jody Hey7pOxOOxA%%' '71111Archive:iubio/evolve/sites/MqOOOS Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SixcutterFreqqM0rOOOd' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1The Hypercard stack calculates the frequency of the various six-cutter restriction enzymes in a few genomes,including bacteriophage lambda, Mus musculus, wheat, E. coli, Saccharomyces, Homo sapiens. The6 O&tO H6algorithm is based on the frequency of dinucleotide pairs.FuOOZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Brian Osborne, bosborne@nature.berkeley.edu7vOPO%%' '71111Archive:iubio/mac/sixcutterfreq*MwPPP# Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Sneath STW0xPP%P4' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Statistical programs to screen a matrix of molecular sequences for atypical sequence comparisons, and tosimulate the addition of constant sites to randomly-placed differences in a molecular sequence comparison.FzP&PHZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:P.H.A. Sneath, mjs@le.ac.uk7{PIPZPIi%%' '71111Archive:iubio/ibmpc/sneathst*M|PZPkPZz Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SolupredvM, W0}PlP}Pl' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This spreadsheet allows one to predict the solubility of recombinant proteins in E. coli based on the aminoacid content.F P}PZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Roger Harrison & Dan Diaz, BL275@cleveland.freenet.edu7 PPP%%' '71111Archive:iubio/mac/solupred-mac*, ibmpc/solupred*M PPP Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SorFindW0 PPPÀ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1SorFind is a DOS program that adds to DNA sequence files a feature table to annotate the location ofputative coding exons. F PPZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Gordon B. Hutchinson, hutch@netshop.bc.ca7PQ P%%' '71111Archive:iubio/ibmpc/sorfind*, ebi/dos/sorfin*MQ QQ ) Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1SpectrumsM, W0QQ,Q;' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Spectrum is a Macintosh and MS Windows program to read in phylogenetic data in Nexus format, anddisplay the bipartition spectra corresponding to the data. It can also be used to find the tree whoseexpected spectrum is closest to the observed spectrum. It outputs spectra in Microsoft Excel and otherformats.FQ,QrZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Michael Charleston, Roderic Page, m.a.charleston@bio.gla.ac.uk7QrQQr%%' '71111Home:http://taxonomy.zoology.gla.ac.uk/mike/spectrum/MQQQ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Spombe-StrainjM0QQQ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1S.pombe strain collection is a Hypercard stack for cataloguing the genotypes of S.pombe yeast strains. Itis adapted from Kai-Uwe Fr?lich's yeast strain.FQQZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Doug Drummond ddrummon@fs2.scg.man.ac.uk7QQQ%%' '71111Archive:iubio/mac/spombe-strain*MQQQۀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1ssu rRNAM0QQQ ' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This Hypercard stack contains the entire Ribosomal Database Project sequence release 1. The sequences areaccessible via a series of linked phylogenetic trees, a list, or by name.FQR!Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:James W. Brown, jwbrown@mbio.ncsu.edu7R!R2R!A%%' '71111Archive:iubio/mac/ssu-rrna*MR3RDR3S Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Swiss-PdbViewerLM, W0RDRURDd' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Swiss-PdbViewer is an application that can display PDB files. Several proteins can be analyzed and can be"piled-up" in 3D space. Differences can be calculated on selected amino acids of the aligned proteins, for6 Rg&RU H6comparison of active sites. It can also measure distances, angles, torsions angles between atoms as well asadd/remove amino acids from the view. It includes many other features.FRVRZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Nicolas Guex, Manuel Peitsch, ng45767@ggr.co.uk7RRR#%%' '71111Home:ftp://expasy.hcuge.ch/pub/PDBViewers/Prot3Dviewer,R4' 'http://www.expasy.ch/spdbv/mainpage.html,http://www.pdb.bnl.gov/expasy/spdbv/mainpage.htmARR Z ##' 'A1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1tacg}M, W, O0RSRi' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for restriction enzyme and other analyses of DNA. This is a command-line program that can beused from MacOS, Wintel through others such as SeqPup.FSS&Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Harry Mangalam, mangalam@uci.edu7S&S7S&%%' '71111Home:http://hornet.bio.uci.edu/~hjm/projects/tacg/7S8SIS8%%' '71111Archive:iubio/restrict-enz/tacg*MSISZSI Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1TFPGAW0 S[SlS[' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1TFPGA (Tools for population genetic analyses) is a Windows program for the analysis of allozyme andmolecular population genetic data. The program calculates simple descriptive statistics, genetic distances,and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, population differentiation andperforms UPGMA clustering and Mantel Tests.F SlSZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Mark P Miller, mpm2@nauvax.ucc.nau.edu7 SSS)%%' '71111Home:http://dana.ucc.nau.edu/~mpm2M SSS; Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1TopPredIIM0 SSSՀL' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Prediction of transmembrane segments in integral membrane proteins, and the putative topologies.FSSZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Claros M.G & von Heijne G., claros@cica.es, gvh@cbs.ki.se7ST So%%' '71111Archive:ebi/mac/, iubio/mac/toppred*MT TT  Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1TOPSW, O0TT,T' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Program to automatically generate and edit protein topology cartoons. These cartoons are two dimensionalrepresentations of the secondary structure of proteins. FT-TOZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Tom Flores, flores@ebi.ac.uk7TPTaTP%%' '71111Home:ebi/pub/contrib/TOPSMTaTrTa؀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Tree Draw DeckeM0TsTTs' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A Hypercard stack which draws phylogenetic trees. It is derived from Drawgram and Drawtree of Phylip byJ. FelsensteinFTTZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:D. Gilbert, software@bio.indiana.edu7TTT%%' '71111Home:iubio/mac/treedraw*7TTT0%%' '71111Archive:ebi/mac/treedraw*MTTTʀA Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1TreeconW0TTTS' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A package for the construction of phylogenetic trees. Its advantages include menu-driven, easy-to-useinterface, quick, handles large datasets, large set of distance-measure methods and distance-matrix based treeconstruction tools, sophisticated options like subset resampling and test of outgroup influence, additional6 U& U3 H6tools like production of partial alignments and indication of informative positions.FTUCZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Yves Van de Peer, yvdp@reks.uia.ac.be7UCUTUC%%' '71111Home:ftp://uiam3.uia.ac.be/7UUUfUU#%%' '71111Archive:iubio/ibmpc/treecon*MUfUwUf4 Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1TreeViewsM, W0UxUUxF' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A program for drawing phylogenies on MacOS and MS Windows. The program reads NEXUS, PHYLIP,Clustal W and similar tree formats. FUUZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Roderic D M Page, r.page@bio.gla.ac.uk7UUUz%%' '71111Home:http://taxonomy.zoology.gla.ac.uk/rod/treeview.html7UUU%%' '71111Archive:iubio/mac/treeview*, iubio/ibmpc/treeview*M UUUπ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1VisedW0 UUU' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A visual sequence editor/display software for Windows, including effective and easy-to-use interface. Features include edit up to 200 sequences of 18,000 bases; powerful pattern search function; support formany sequence file formats; supports extraction of sequences from library files; figure preparation; boxedoutput of sequence identities; imports MACAW alignments; protein sequence prediction in one or all sixframes.F UVIZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ken Peters, kpeters@qb.island.net7 VJV[VJ%%' '71111Archive:iubio/ibmpc/vised*M V[VlV[) Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Visual BLAST and FastA6W0VmV~Vm;' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1These programs are designed for interactive analysis of full BLAST and FASTA output files containingprotein sequence alignments. They implement analytical tools which automate detailed analysis of BLASTand FASTA outputs, and include tools for multiple alignment analysis.FV~VZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Patrick Durand et al., durand@lmcp.jussieu.fr7VVV%%' '71111Home:http://www.lmcp.jussieu.fr/~durand/MVVVĀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1WinDotW0VVV' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1A dotplot program for MS Windows.FVVZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ramin Nakisa, ramin@ic.ac.uk7VW V%%' '71111Archive:iubio/ibmpc/windot, ebi/dos/windotMW WW ؀ Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1WinMGMW0WW-W' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1Visualisation and manipulation tools for proteins, nucleic acids and organic molecules, includingmanipulation of molecules represented as CPK, stick and ball, ribbons and cylinders, and colorations byatomic type, atoms of a selected area, of an active site, and others. Several other features are included.FW-WaZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Mehdi Rahman, Robert Brasseur, mehdirah@fsagx.ac.be7WbWsWb0%%' '71111Home:http://www.fsagx.ac.be/info_faculte/info_dep/info_bp/mehdi/winmgm/winmgmen.htmMWsWWsA Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1WinSeq~W, O0WWWS' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1The ReadSeq program for converting among biosequence file formats, for MS Windows.FWWZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ramin Nakisa, ramin@ic.ac.uk7WWWv%%' '71111Archive:iubio/ibmpc/winseq, ebi/dos/winseq, see iubio/readseq/ for others~WWW W&!!W H Z ##' '~1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1WPDBWÿ0WWW' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1WPDB (the Protein Data Bank through MS Windows) is a package with a compressed version of PDB and aset of tools to query features of a single structure or perform a comparative analysis on multiple structureswith emphasis on sequence alignment and structure superposition.FWX Z  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Ilya N. Shindyalov, Philip E. Bourne, bourne@sdsc.edu7X!X2X!F%%' '71111Home:ftp://ftp.sdsc.edu/pub/sdsc/biology/WPDB/MX2XCX2W Z ##' 'M1ͪZZZ   +$$Z$$+Ы11ZZ   qZ$Hl Dh@dq1Yeast StrainvM0XDXUXDi' '01ͪ   +Z$$Z$$+Ы11  qZ$Hl Dh@dq1This is a Hypercard stack for cataloguing XUXfthe genotypes of S. cerevisiae yeast strains.FXgXxZ  ##%%' 'F1ͪZZZ &Z$$$$&Ы11Z q$Hl Dh@dq1Author:Kai-Uwe Froehlich, cbkfr01@mailserv.zdv.uni-tuebingen.de7XxXXx%%' '71111Archive:iubio/mac/yeaststrain*, ebi/mac/M XXX Z ##''M1ͪZZZ  &$$Z$$&  Ы 11ZZ     qZ$Hl Dh@dq1 0 XXX' '0 ŀ1ͪ  Ы11  1Index0 XXXӀ' '01ͪ    Ы 11     1Bio Catalog of software 20 XXX' '0Citing software 8 XXclient-server 5XXClustal 5XYCORBA 7YYEMBOSS 5YY&Entrez 6Y&Y7European Bioinformatics Institute (EBI) 2Y8YIFile Transfer Protocol (FTP) 3YIYZfree software 1Y[Ylgenome data 6YlY}Hypertext Transport Protocol (HTTP) 3Y~Yimage analysis 6YYIUBio Archive 2YYJava 4YYMacintosh 1YYMicrosoft 1YYmolecular modelling 7YYMulti-platform software 4YZ National Center for Biotechnology Information (NCBI) 6Z ZNIH Image 6 ZZ,PHYLIP 6! 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