Date: Wed, 07 Jan 2004 15:33:11 -0500 Subject: Re: software submission request From: Charles Crane To: Don Gilbert Dear Don Gilbert, The archive flipperiu.tar.gz contains source and configuration files for my genetic mapper. Attached to this e-mail is the abstract file that goes with it. Is there anything else that I need to do for now to get this on your FTP site? I will be demonstrating this software at Plant and Animal Genome XII next week. What is the exact FTP site that I should send users to to get this tarball? Thank you for your help! --Charles Crane Here is an annotated directory of this archive. bcsddoubnegsimulator.cpp: program to simulate a backcross population where two particular loci are always deleted bcsddoubrxsimulator.cpp: program to simulate a backcross population with selection directly against recombination between two loci bcsddoubsimulator.cpp: program to simulate a backcross population where two particular loci are never deleted bcsdtripsimulator.cpp: program to simulate a backcross population where three particular loci are never deleted bcsegdissimulator.cpp: program to simulate a backcross population with selection at a single locus bcsimulator.cpp: program to simulate a backcross population comparemaps.c: program to compare estimated with true map order in simulations delsimulator.cpp: program to simulate a deletion population inbrsimulator.cpp: program to simulate an inbred population mapfromfile6.cpp: the mapper itself parsemmraw.pl: script to reformat a MapMaker3 raw data file as a Flipper input data file rfbcptrirunroot.cfg: example of a configuration file used by the mapper for a backcross population. This file and the next were used for the same simulation. rfbcptrisimroot.cfg: example of a configuration file used by bcsimulator.cpp rfdelptvvrunroot.cfg: example of a configuration file used by the mapper for a deletion population. This file and the next were used for the same simulation. rfdelptvvsimroot.cfg: example of a configuration file used by delsimulator.cpp rfinbrptrmrunroot.cfg: example of a configuration file used by the mapper for an inbred population. This file and the next were used for the same simulation. rfinbrptrmsimroot.cfg: example of a configuration file used by inbrsimulator.cpp runwrapper1.pl: script to simulate a mapping population, run the mapper on it, and compare estimated with true map order runwrappererrd.pl: script to simulate a mapping population, introduce typing errors, run the mapper on it, and compare estimated with true map order runwrappermissd.pl: script to simulate a mapping population with missing data, fill in missing data, run the mapper, and compare estimated with true map order runwrappersgd.pl: script to simulate a mapping population with segregation distortion at a single locus, run the mapper on it, and compare estimated with true map order runwrappersgdoub.pl: script to simulate a backcross mapping population in which two loci are never deleted, run the mapper on it, and compare estimated with true map order runwrappersgdoubneg.pl: script to simulate a backcross mapping population in which two loci are always deleted, run the mapper on it, and compare estimated with true map order runwrappersgdoubrx.pl: script to simulate a mapping population with selection against recombination between two loci, run the mapper on it, and compare estimated with true map order runwrappersgtrip.pl: script to simulate a backross population in which three loci are never deleted, run the mapper on it, and compare estimated with true map order sumposrecs.c: program to combine *posrec* files from multiple mapping populations. One can then run the mapper on the combined *posrec* file to benefit from parallel processing in the assembly of the array of recombination fractions, which is the rate-limiting step for the mapper. worklist1105a.txt: file used by runwrapper1.pl to perform a series of population simulations, maps, and comparisons worklist1218c.txt: file used by runwrappermissd.pl to perform a series of population simulations, maps, and comparisons, with missing data worklist1220a.txt: file used by runwrappererrd.pl to simulate a series of populations with typing errors, map them, and compare maps Note about *data* and *posrec* files: One needs to be careful with these when running multiple mapping populations. The runwrapper1.pl script is set up to reuse the name of its *data* file, but the scripts and programs in this distribution do not reuse the name of the *posrec* file. These files tend to be very large, and a seemingly harmless transect in some variable can easily fill up a multigigabyte filesystem if all of these files are preserved. If one is not doing parallel processing, there is no need to print out the *posrec* file, and one can comment out the block of lines where it is written to the filehandle NGR in mapfromfile6.cpp. Please report any bugs or suggestions to: Charles Crane, USDA-ARS Department of Botany and Plant Pathology Purdue University 915 W. State Street W. Lafayette, IN 47907-2054 ccrane@purdue.edu A manuscript containing the algorithm and results of various simulations with population size, segregation distortion, missing data, typing errors, population type, and uniform versus random marker distribution, is being submitted to Genome Research: Crane, C. F., and Crane, Y. M. A nearest-neighboring-ends algorithm for genetic mapping.