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Botanical Software ?

Tony Travis ajt at rri.sari.ac.uk
Fri Jan 14 09:24:27 EST 1994


Frank Scherenschlich (scheren at de.uni-paderborn.pbemt2) wrote:
: Last year I found a note about a file named 'A Guide to Botanical Software for
: MS-DOS Computers' you can get from J-P Frahm at hh216fr at duc220.uni-duisburg.de. But
: it seems that this guy doesn't work any longer with his computer. Is there someone
: else who has this file?


Here it is:


 



A Guide to Botanical Software

for MS-DOS Computers




Public Domain and Shareware









Version 1.0










Jan-Peter Frahm


Duisburg 1991



c 1990 Jan-Peter Frahm










CONTENTS



Preface										5
Description of Programs								6
Resource Directory									24
Bibliography 										26
Alphabetical Index									28
Subject Index										29


PREFACE




This compilation of computer programs for botanical applications is based on a list of software, which was made available for ASK, the Academic Software Cooperation of the University of Karlsruhe. ASK is accessible by Internet (details see note under "Resource Directory") and has implemented a retrieval system to search software for specific needs. Therefore the format of the description of programs is similar to the ASK system.
The present list has been extended and is available from the author on disk or by e-mail.
The documentation of the programs needs no explanation. 
Included are
- freeware or public-domain programs, which may generally be copied free,
- shareware programs, which may be copied free and used for evaluation purposes. If they are, however, used, a registered version must be bought from the author. The prices are often given in US $ and therefore only approximate in programs distributed outside the US, and
- demo versions of programs with limited facilities. Full versions have also to be ordered from the author.
All programs are available from the sources listed in the resource directory. They can be obtained on disk mainly through the software library of the International Association of Bryologists, but also from the authors, and by file transfer from fileservers.
The purpose of this list is to give botanists working in classical disciplines such as systematics, ecology and phytogeography an overlook of software sources which can be used free or free for trial purposes. Not included are programs for general scientific work such as statistics or bibliographies, programs which are sold commercially, programs for special disciplines such as phytochemistry, chromatography or similar,  and datafiles. The list is especially important for special applications, which hardly can be solved by commercial programs (e.g. herbarium labels, herbarium management), but also in countries, where software is not widely known and distributed. The philosophy behind is that software is a tool for science and science shall be promoted by providing programs at no or low costs. Therefore all additions to this list are welcome.



Jan-Peter Frahm
Universitaet Duisburg,
Fachbereich 6, Botanik
Postfach 101503
4100 Duisburg
Phone X203/379-2712
Fax -3333 or -2108
Telex 855 793 uni du d
E-mail hh216fr at unidui.uni-duisburg.de

1
Title:			PANKEY
Version 		6.0
Date: 			12/88
Purpose: 		Expert identification program with colour image option
Keyword(s): 		identification
Author: 		Dr.  R. Pankhurst, Dept. of Botany, Natural History Museum, 		Cromwell Road, London SW7 5BD, England
available from: 	author
Progr. language: 	Fortran 77
Number of files: 	12
Size:			335 K
Hardware req.:	EGA or VGA recommended for display of images.
Oper. System:		MS-DOS Author: and higher, Apple Macintosh
Physical carrier:	5,25" floppy disk 360K
Documentation:	41K manual on disk
Price: 			 100
Conditions:  		demo version with data files allowing to identify the British 			orchids and species of the genus Jurinea free from the author or 			(1).
Publication(s): 	Pankhurst, R.J. & Aitchison, R.R. (1975) An on-line identification 			program. Pp. 181-194 in R.J. Pankhurst (ed.), Biological 				Identification with computers. Systematics Assoc. Special Vol.
Remarks: 		Uses DELTA format for taxonomic descriptions.


2
Title:			BIDS
Version 		1.0
Date: 			5/87
Purpose: 		Biological Identification System, a program to identify biological 			specimens
Keyword(s): 	
Author: 		B.J. O'Shea, 131 Norwood Road, London SE 24 9AF, UK
available from: 	1,2,3
Progr. language:	Pascal
Number of files: 	29
Size:			299 K
Hardware req.:	-
Oper. System:		MS-DOS 2.1 and higher
Physical carrier:	5.25" DD disk
Documentation:	65 pp. manual on disk
Price: 			free
Remarks:		Some menu option are not yet supported. Comes with a small 			demonstration set of files for identification of the 23 species of 			Tortula (Musci) in the UK.
3
Title:			KARTSCHL
Version 		
Date: 			8/87
Purpose: 		Program for identification of Swiss mosses
Keyword(s): 	
Author: 		Johannes Geibel, B.P. 705, 1264 St. Cergue, Switzerland
available from: 	1,2,3
Progr. language:	BASICA, with source code
Number of files: 	11
Size:		  	184 K
Hardware req.:	-
Oper. System:		MS-DOS 2.1 and higher
Physical carrier:	5,25" DD floppy disk
Documentation:	manual (8 K) on disk
Price: 			free
Conditions:  		
Publication(s):
Remarks:		Comes with a BASICA program to correct or modify the data 			matrix.


4
Title:			ASKATAXA
Version 		2.2
Date: 			7/87
Purpose: 		Program for identification of plant taxa.
Keyword(s): 	
Author: 		Dr. Fred Rhoades, Biology Dept., Western Washington Univ., 			Bellingham, WA 98225, USA
available from: 	1,2,3
Progr. language:	
Number of files: 	35
Size:			323 K
Hardware req.:	-
Oper. System:		MS-DOS 2.1 and higher
Physical carrier:	5.25" DD floppy disk
Documentation:	52 K manual on disk
Price: 			free
Conditions:  		For the generation of own data sets, the program PC Taxon is 			required.  PC Taxon is available at a price of 90$ from Compress, 			P.O. Box 102, Wentworth, N.H. 03282, USA
Publication(s):
Remarks:		Comes with several datafiles for identification of lichen genera and 			mosses and hepatics of western North America.
			See also the programs "PC TAXON utilities".
5
Title: 			DELTA
Version:	 	3.0
Date: 			1986
Purpose: 		A general system for processing taxonomic descriptions.
Keyword(s): 		Taxonomy
Author: 		 M.J. Dallwitz & T.A. Paine, CSIRO Division of Entomology, 			G.P.O. Box 1700, Canberra, A.C.T. 2601, Australia
available from:	1,2
Number of files: 	48
Size: 			545 K
Oper. System: 		MS-DOS, version for VAX/VMS and PRIME computers also 			available.
Phys. Carrier: 	 5,25" floppy disks 360K (2)
Documentation:	Manual (Dallwitz, M.J. & T.A. Paine 1986: User's Guide to the 			DELTA System. Division of Entomology Report No. 13, 				Commonwealth scientific and industrial research organisation, 			Australia, 106 pp.) available separately from the author. 
Price: 			free 
Publication(s):	Dallwitz, M.J. 1980. A general system for coding taxonomic 			descriptions. Taxon 29: 21-26.
Description:	"A general system for the concise representation and manipulation of taxonomic descriptions. The system is versatile, easy to understand and designed to minimize coding errors. The descriptions can replace natural-language descriptions both at the time of recording and in publications. A format-conversion program, CONFOR, converts the coded descriptions into natural language and into formats required by programs for key-generation, interactive identification, and numerical classification..... The program will help to compile data describing species  i.e. a database and processing it, for keys, classifications and descriptions. For those writing a Flora, handbook or monograph, a revision or a classification." The program KEY generates taxonomic keys. DELTA is compatible with the identification program PANKEY and - with a conversion program - with the cladistic program PAUP.
Remarks: 	Applications of this program are being described in "DELTA Newsletter" edited by Robert D. Webster, USDA/ARS/SBML, Bldg. 265, BARC - East, Beltsville, MD 20705, USA.


6
Title:			MPSORT
Purpose:		Computer aided construction of phytosociological tables.
Keyword(s): 		Plant Sociology, Ecology
Author:		Dr. Bodo Maria Moeseler, Institut fuer Landwirtschaftliche 			Botanik der Universitaet, Meckenheimer Allee 176, D 5300 Bonn, 			Germany
available from:	author; test-version: 1,2.
Number of files:	10
Size:			227K
Oper. System: 		MS-DOS Author: and higher
Software req.:		MS-Multiplan 3.0
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	Manual (72K) on disk
Price: 			$ 90. Test version  free for members of the International 				Association of Bryologists. 
Conditions:		Shareware.  
Publication(s):
Description:	MPSORT is operated like MS-Multiplan and used in the same manner. It is able to work with up to ten different phytosociological scales. The initial able is set up in MS-Multiplan (or another spreadsheet program using the SYLK format) and load into MPSORT. MPSORT  calculates and sorts the table, determines the number of species per relevee, the frequency of each species, the average of dominance, the coexistence of community and the percentage similarity and arranges the species by frequency, average of dominance and alphabetically in different stratifications.
Remarks: 		Special version for the use with MS-Multiplan 4.0 available from 			the author.


7
Title			COENOS
Version		7
Date			1989
Purpose:		A computer program for identifying species-relevee groups in 			vegetation studies.
Keyword(s) 		Biology. Ecology, Plant-sociology.
Author:		 Adolf Ceska, P.O. Box 1761, Victoria, B.C., Canada V8W 2Y1
available from:	author, demo from 1,2
Progr.language:	FORTRAN IV 
Number of files:	6
Size:			141K
Hardware req.:
Oper. System: 		MS-DOS Author: and higher
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	none, online help built in program.
Price: 			90$, Demo version allowing to run 50  relevees and 200 species 			free.
Publication(s):	Ceska, A. & H. Roemer 1971. Vegetatio 23:255-27
8
Title:			TREESEARCH
Version:		1.0
Date:			3/89
Purpose:		A program to construct phylogenetic trees.
Keyword(s) 		Biology, Zoology, Botany, Cladistics, Phylogeny
Author:		 Dr. R.W. Bruggeman, Mathematical Institute, Budapestlaan 6, 			Utrecht, The Netherlands.
available from:	1,2
Progr.language:	Turbo-Pascal 4.0
Number of files:	12 incl. test files.
Size:			294 K
Hardware req.:	no coprocessor required
Oper. System: 		MS-DOS 2.1 and higher
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	Manual (9pp.) available from the author.
Price: 			free 
Conditions:		Public Domain
Publication(s):
Description:
Remarks: 		Also version for Atari ST available from the author.


9
Title: 			DECORANA, TWINSPAN
Version: 		3
Dat:e 			1987-89
Purpose:		Detrended correspondence analysis and two way indicator species 			analysis.
Keyword(s): 		biology, ecology, systematics, phenetics, taxonomy,  multivariate 			analysis
Contact: 		Dr. J. Birks, Botanical Institute, University of Bergen, Allegaten 			41, N 5007 Bergen, Norway
available from:	1,2
Author:		 M.O.Hill, Cornell University
Progr.language:	FORTRAN compiled
Number of files:	8 (with demofiles)
Size:			317K
Hardware req.:	math coprocessor
Oper. System: 		MS-DOS 2.1 and higher
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	39 K on disk
Price: 			free 
Conditions:
Publication(s):
Description:		TWINSPAN is a program for arranging multivariate  data in an 			ordered two way table by classification of the individuals and 			attributes. The two way classification makes possible a tabular 			matrix arrangement which approximates the result of Braun-			Blanquet tablework. DECORANA is designed to make ordinations 			of data on the occurrence of a set of species in a set of samples.
Remarks: 		DECORANA and TWINSPAN are  two of the Cornell University 			ecology programs. Version for mainframe computers, version not 			requiring a math coprocessor and the FORTRAN source code also 			available on request. Comes with CONDENSE by S.B. Singer and 			H.G. Gauch, an utility program for converting data matrices into 			the format required. 


10
Title: 			HERBARIUM MANAGER
Version: 		1.0
Date: 			3/88
Purpose:		A program to handle loans, exchanges and other functuons of large 			herbaria.
Keyword(s): 		biology, botany, taxonomy, herbaria
Author:		 Dr. Barbara M. Thiers, The New York Botanical Garden, Bronx, 			N.Y. 10458, USA
available from:	1,2
Progr.language:	dBase
Number of files:	186
Size:			555K
Hardware req.:	
Oper. System: 		MS-DOS 2.1 and higher
Software req.:		dbase III+
Phys. Carrier: 	5,25" floppy disk 360K (2)
Documentation:	80 K on disk
Price: 			free 
Conditions:
Publication(s):
Description:		DBase III+ application for all record keeping functions of the New 			York Botanical Garden with regard to loans, exchange, gifts etc., 			with introduction and step by step instructions.
Remarks: 


11
Title:			DMAP 
Version: 		2.0
Date: 			5/89
Purpose:		a computer program for sitsribution and coincidence map plotting
Keyword(s) 		biology, botany, distribution
Author:		Dr. Alan Morton, Dept. of Pure and Applied Biology, Imperial 			College, Silkwood Park, Ascot, Berks, SL5 7PY, UK
available from:	author, test version from 1,2
Progr.language:
Number of files:	23
Size:			257 K
Hardware req.:	
Oper. System: 		MS-DOS 2.1 and higher
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:
Price: 			$ 20
Conditions:		shareware
Publication(s):
Description:		A program for distribution mapping at any scale. Automatically 			superimposes a numbered grid. A range of symbol types is 				available, and the size of symbols is user-defined. With facility for 			coincidence mapping of groups and species.. Runs on all 				commonly fitted graphics displays. Supports 24 and 9 pin dot-			matrix printers, and also Hewlett-Packard-compatible ink-jet and 			laser printers giving high resolution publication quality maps.
Remarks: 		Comes with a test-data-set.


12 
Title: 			LOAN
Version: 
Date: 			6/88
Purpose:		A program to handle herbarium loans
Keyword(s) 		biology, botany, herbaria
Author:		Prof. Dr. G. Wagenitz, Systematisch-Geobotanisches Institut der 			Universitt, Untere Karspuele 2, D 3400 Goettingen, Germany
available from:	1,2
Progr.language: 	dBase
Number of files:	11
Size:			68K
Hardware req.:	
Oper. System: 		MS-DOS 2.1: and higher
Software req.:		dBase III+
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	4K on disk
Price: 			free 
Conditions:		Public Domain
Publication(s):
Description:		An easy to operate program to print loans. Special features are 			automatical numbering of loans, address file with 80 herbaria (can 			be extended), search for genera on loan, listing of loans due for 			return. 
Remarks: 		Original version with dialogue in German. English version can be 			provided on request as well as a modified version for the 				Herbarium of the University of Alberta with some more fields for 			number of parcels and calculating exchange-balance. The loan 
			form can easily be adapted with a text editor.


13
Title:		 	BACCHUS
Version: 		4.0
Date: 			11/88
Purpose:		A program for maintaing a small herbarium.
Keyword(s) 		biology, botany, herbaria, labels
Author:		B.J.O'Shea. 131 Norwood Road, London SE24 9AF, UK
available from: 	1,2
Progr.language: 	BASIC, without source code
Number of files:	14
Size:			519 K
Hardware req.:
Oper. System: 		MS-DOS 2.1 and higher
Phys. Carrier: 	5,25" floppy disk 360K (2)
Documentation:
Price: 			free 
Conditions:
Publication(s):
Description:
Remarks: 		Includes a variety of printed reports, including labels.


14
Title:			CURATOR 
Version: 
Date: 			12/85
Purpose:		A set of programs for labels and loans.
Keyword(s) 		biology, botany, herbaria, labels
Author:		developed by Dept. of Botany,  University of Michigan.
available from:	1,2
Progr.language:	dBase II
Number of files:	100
Size:			230 K
Hardware req.:
Oper. System: 		MS-DOS 2.1 and higher
Software req.:		dBase II
Phys. Carrier: 		5,25" floppy disk 360K (2)
Documentation:	12 K on disk
Price: 			free for members of the International Association of Bryologists, 			fee for copying and mailing for non-members $6 (prepaid, cheque)
Conditions:
Publication(s):
Description:
Remarks: 


15
Title: 			CLUSTER 
Version: 		4.0
Date: 			10/87
Purpose:		Program to generate trees on similarity coefficient.
Keyword(s) 		biology, taxonomy, phenetics
Author:		 B.J. O'Shea, 131 Norwood Road, London SE24 9AF, UK
available from:	1,2
Progr.language:	BASIC, source code and compiled
Number of files:	5 (incl. test file)
Size:			106 K
Hardware req.:
Oper. System: 		MS-DOS 2.1 and higher
Phys. Carrier: 		5,25" floppy disk 360K
Documentation:	none
Price: 			free 
Conditions:
Publication(s):
Description:		A simple to use cluster analysis program for calculating trees for 			phenetics with menus, allowing maintenance of a data matrix, 			manipulations of data using different primary characters, printing 			of dissimilarity coefficients, display and printing of dendrograms.
Remarks: 		This program is developed on the basis of a Commodore Basic 			program by J.-P. Frahm. Another realisation of the same source 			code in Pascal written by W. VanMaele is available on request. 			The latter allows in addition a different weighting of characters 			and requires CGA for display of the dendrogram.


16
Title: 			LAB
Version: 		2.2
Date: 			9/90
Purpose:		Herbarium Label Program
Keyword(s) 		biology, botany, labels
Author:		 B.J. O'Shea, 131 Norwood Road, London SE24 9AF, UK
available from:	1,2
Progr.language:	TURBO-BASIC, with source code
Number of files:	11
Size:			178 K
Hardware req.:
Oper. System:	 	MS-DOS 2.1 and higher
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	6 K on disk
Price: 			free 
Conditions:
Publication(s):
Description:		Allows to print either 40 normal or 60 condensed characters per 			line for more information storage. Defaults are shown on screen. 			With multilingual dialogue and comfortable options such as 			automatically centering of headers, bold and underlined print, two 			column print on dot matrix and laserprinters
Remarks: 


17
Title:			HERBAR 
Version: 	
Date: 			6/89
Purpose:		A herbarium record keeping program with label printing
Keyword(s): 		biology, botany, labels, floristics, herbaria
Author:		 R. May, Bundesanstalt fr Naturschutz und Landschaftspflege, 			Konstantinstr. 110, D 5300 Bonn 2, Germany
available from:	1,2
Progr.language:	dBase
Number of files:	17
Size:			32 K
Hardware req.:
Oper. System:	 	MS-DOS 2.1 and higher
Software req.:		dBase III+
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	none
Price: 			free 
Publication(s):
Description:		A program for herbarium records with fixed fieldlength. Supports 			two different label formats, which can be modified to own 				requirements and formats. The programs allows the input of label 			data, print of any record in any number in different printforms, to 			print and modify the last entry, replace, append and print any 			record.
Remarks: 		Original with dialogue in German.  English version by J.-P. Frahm 			on request. An enhanced and debugged version by B.J. O'Shea, 			which runs also under dBase IV, has additionally report functions 			to list species per locality and species according to collection 			numbers. A compiled version is available from the author.


18
Title: 			PST
Version: 		2.0
Date: 			3/87
Purpose:		Program to sort plant sociological tables
Keyword(s) 		biology, botany, ecology, plant sociology
Author:		Dr. R. Callauch, Systematisch-Geobotanisches Institut der 				Universitaet, Untere Karspuele 2, D 3400 Gttingen, Germany
available from:	test version from 1,2
Progr.language:	Pascal, with source code
Number of files:	10
Size:			256 K
Hardware req.:
Oper. System: 		MS-DOS 2.1 and higher
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	online help
Price: 			$ 90, test version free
Conditions:		shareware, registration with the author.
Publication(s):	Callauch, R., Stallmann, G. Die Anfertigung 					pflanzensoziologischer Tabellen mit der neuen PST Version 2.0, 			Tuexenia 7: 497-498,1987
Description:		A program to sort up to 100 relevees with up to 100 species each. 			Fully menu driven, with help key. Sorts taxa automatically 				according to abundance and the relevees after similarities of 			ecological factors such as humidity factors, pH values etc. 				Dialogue in German.
Remarks:


19
Title:			KEYOUT
Version:		1.0
Date:			3/88
Purpose:		Program for identification of plants
Keyword(s) 		biology, taxonomy, identification
Author:		Dr. Janice M. Glime. Dept. of Biologal Sciences, Michigan 			Technological University, Houghton, MICH 49943, USA
available from:	1,2
Progr.language:
Number of files:	32 incl. several test-files
Size:			261 K
Hardware req.:
Oper. System: 		MS-DOS 2.1 and higher
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	none
Price: 			free 
Conditions:
Publication(s):
Description:		Identification program for students with a matrix of 121 flowering 			plant families and an acrocarpous bryophyte data set. It allows the 			instructor to provide up to 10 numbered specimens for testing 			purposes and tell the computer the family or genus number each. 			When the student enters the specimen number, the computer will 			tell the student each time he or she chooses an inappropriate 			character. 
Remarks: 


20
Title:			MEKA 
Version: 		1,2
Date: 	
Purpose:		A general purpose multiple entry key algorithm and editor.
Keyword(s) 		biology, identification
Author:		Thomas Duncan & Christopher A. Meacham, University 				Herbarium, University of California, Berkeley, CA 94728, USA
available from:	1,2
Progr.language:	Turbo-Pascal, with Source Code
Number of files:	13
Size:			295 K
Hardware req.:
Oper. System: 		MS-DOS 2.1 and higher, also versions for CP/M machines 				available from the authors. 
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:	45 K on disk
Price: 			free 
Conditions:
Publication(s):
Description:
Remarks: 		Comes with MEKAEDIT V. 1.0 which allows users to make their 			own keys for access by MEKA. 


21
Title:			MAPPING 
Version: 	
Keyword(s):
Date: 			4/91
Purpose:		Distribution mapping of plants and animals on the basis of  			coordinates of the UTM or German gridmap system 1:25000.
Keyword(s) 	 	biology, mapping, botany, zoology
Author:		Martin Wiemers, Kleikamp 13, D 4400 Muenster, Germany
available from:	test version from 1,2
Progr.language:
Number of files:
Size:			221 K compressed
Hardware req.:	colour display with VGA and EGA; supported: mouse, EMS.
Oper. System: 		MS-DOS 2.1 and higher
Phys. Carrier: 	5,25" floppy disk 360K
Documentation:
Price: 			200 $ for full version, demo version (with limited number of 			entries) free 
Conditions:
Publication(s):
Description:
Remarks: 		Comes with test maps of North-Rhine-Westphalia and the Canary 			Islands.


22
Title:			PAUP
Version 		3.0
Date: 			11/86
Purpose: 		Phylogenetic Analysis using Parsimony
Keyword(s): 		Cladistics
Author: 		D.L. Swofford, 607 East Peabody Drive, Champaign, Illinois 			61820, USA
available from: 	1,2,3 (evaluation copy)
Progr. language:	Turbo-Pascal
Number of files: 	571 K
Size:			234 K
Hardware req.:	Coprocessor required
Oper. System:		MS-DOS 2.1 and higher
Physical carrier:	three 5,25" DD floppy disks
Documentation:	
Price: 			50$
Conditions:  		Shareware
Publication(s):	Platnick, N.I. 1988. Programs for quicker relationships. Nature 			335: 310.
Remarks:


23
Title:			CHOROL
Version 		1.1
Date: 		
Purpose: 		Program to plot  distribution maps on Flora Neotropica base maps
Keyword(s): 	
Author: 		D. Ebster & W. Morawetz, Botanisches Institut, Rennweg 14, A 			1030 Wien, Austria
available from: 	Dr. Morawetz
Progr. language:
Number of files: 	
Size:		
Hardware req.:	
Oper. System:	
Physical carrier:	
Documentation:	
Price: 			offered as free in the Flora Neotropica News
Conditions:  	
Publication(s):	 
Remarks:


24
Title:			PC TAXON UTILITIES
Version 		
Date: 			6/89
Purpose: 		The programs MAKETAXN and MAKEDELT convert files 			between the taxonomic programs PC Taxon (see note under 			ASKATAXA) and DELTA
Keyword(s): 	
Author: 		Dr. F. Rhoades,  Biology Dept., Western Washington Univ., 			Bellingham, WA 98225, USA
available from: 	author
Progr. language:
Number of files: 	5
Size:			108K
Hardware req.:	
Oper. System:	
Physical carrier:	
Documentation:	4K on disk
Price: 			
Conditions:  	
Publication(s):	
Remarks:


25
Title:			COENOSIS-2
Version 		
Date: 			8/87
Purpose: 		Program for classification of ecological data
Keyword(s): 		Ecology
Author: 		E. Escurra & M. Equihua
Contact:		M. Equihua, 4 McHughCourt, Heslington, York Y01 5EP, UK
available from: 	1,2,3
Progr. language:	Pascal
Number of files: 	5
Size:			35K
Hardware req.:	
Oper. System:	
Physical carrier:	
Documentation:	
Price: 			free
Conditions:  	
Publication(s):	 Escurra, E. & M. & M. Equihua. La teoria de informacion 				aplicada a la classificacion de datos biologicos. In: Metodos 			cuantitativos en la biogeografia. Publ. # 12, Instituto de Ecologia, 			Universidad Nacional de Mexico..
Remarks:


26
Title:			TROPICOS
Version 		
Date: 		
Purpose: 		Botanical Database System
Keyword(s): 		Taxonomy, Floristics, database, herbaria
Author: 		Dr. R.E. Magill, Missouri Botanical Garden, P.O.Box 299, St. 			Louis, Missouri , USA
available from: 	author
Progr. language:
Number of files: 	
Size:		
Hardware req.:	
Software req,:		Runtime version of database program Revelation 
Oper. System:	
Physical carrier:	on disks 5.25" or 3.5" any density
Documentation:	manual separetely
Price: 			free, runtime version of Revelation US $ 150
Conditions:  	
Publication(s):	TROPICOS brochure published by the Missouri Botanical Garden.
Remarks:		TROPICOS is the taxonomic and floristic database system of the 			Missouri Botanical Garden. Data on bryophytes and flowering 			plants stored at the Botanical Garden can be provided on request. 
27
Title:			HERB
Version 		
Date: 			6/87
Purpose: 		Herbarium Maintenace System
Keyword(s): 	
Author: 		B.J. O'Shea, 131 Norwood Road, London SE24 9AF, UK
available from: 	1,2,3
Progr. language	dBase III+:
Number of files: 	11
Size:			264K
Hardware req.:	
Oper. System:		
Physical carrier:	1 floppy disk 5,25"
Documentation:	36K on disk
Price: 			free
Conditions:  	
Publication(s):
Remarks:


28
Title:			PHYLIP
Version 		3.0
Date: 			4/87
Purpose: 		Phylogeny Interference Package
Keyword(s): 		Cladistics
Author: 		Dr. Joseph Felsenstein, Dept. of Genetics, University of 				Washington, Seattle, Wash. 98195, USA
available from: 	1,2,3
Progr. language:
Number of files: 	65
Size:			ca. 2 MB
Hardware req.:	
Oper. System:		
Physical carrier:	
Documentation:	135 K on disk
Price: 			free
Conditions:  	
Publication(s):
Remarks:		A package of 26 programs


29
Title:			HERBLABEL
Version 		2
Date: 			2/88
Purpose: 		Herbarium Label Program
Keyword(s): 	
Author: 		Dr. Janice M. Glime, Dept. of Biol. Sciences, Michigan 				Technological University, Houghton, Michigan.
available from: 	1,2,3
Progr. language:
Number of files: 	11
Size:			313K
Software req.:		MS-Word recommended for printing and support of different fonts
Oper. System:	
Physical carrier:	1 floppy disk 5,25"
Documentation:	
Price: 			free
Conditions:  	
Publication(s):
Remarks		A spellchecker for latin species name of  the mosses and heaptics 			of North America, Europe and Japan is available in addition.:


30
Title:			LEAFDEMO
Version 		1.0
Date: 		
Purpose: 		display of leaf shape on screen according to measuremnets of 			length and width, determination of leaf form
Keyword(s): 	
Author: 		Dr. A.M.Empain, Jardin Botanique National de Belgique, 				Domaine de Bouchout, B 1860 Meise
available from: 	1,2,3
Progr. language:	Forth
Number of files: 	16
Size:			203 K
Hardware req.:	CGA recomended, emulator for hgc on disk
Oper. System:		
Physical carrier:	1 5,25" disk
Documentation:	8K on disk
Price: 			 free
Conditions:  	
Publication(s):	Empain,A. 1987: Shape of moss leaves: a versatile method of 			description. Bulletin du Jardin Botanique National de Belgique 			57:331-361.

Remarks:


31
Title:			SIDGEND2
Version 		
Date: 			1/86
Purpose: 		Calculating Nei's genetic distance
Keyword(s): 	
Author: 		Paul W. Sattler & Larry R. Hilburn
available from: 	1,2,3
Progr. language:	BASIC, not compiled
Number of files: 	5
Size:			 
Hardware req.:	
Oper. System:		
Physical carrier:	1 5,25" disk
Documentation:	5K on disk
Price: 			 free
Conditions:  	
Publication(s):	Paul W. Sattler and Larry R. Hilburn, Journal of Heredity 76:400 			(1985)


32
Title:			LABELS3
Version 		
Date: 			9/86
Purpose: 		A herbarium label program
Keyword(s): 	
Author: 		J. Beaman
available from: 	1,2,4,5
Progr. language:	dBase III+
Number of files: 	47
Size:			269 K 
Software req.:		WordStar
Oper. System:		
Physical carrier:	1 5,25" disk
Documentation:	5K on disk
Price: 			 free
Conditions:  	
Publication(s):	




Sources:


(1) Programs available from International Association of Bryologists, software library, Prof. Dr. Jan-Peter Frahm, Universitaet Duisburg, Fachbereich 6, Botanik, Postfach 101503, 4100 Duisburg, Germany. Phone X49-203-379-2712, fax -3333 or - 2108, e-mail hh216fr at unidui.uni-duisburg.de.
Copy of the program free for members of the International Association of Bryologists, fee for copying and mailing for non-members $6 (prepaid, cheque).

(2) Programs can be downloaded from IBIS, the International Bryological Information System installed on a CONVEX host computer at the University of Duisburg. For the access, a usercode and a password is necessary, which can be obtained by e-mail
from Jan-Peter Frahm (hh216fr at unidui.uni-duisburg.de). Login  is possible by the telnet command (use: telnet hostname or telnet IP number, the name of the host is duc220.uni-duisburg.de, IP number is 134.91.4.5), o with Datex-P (x29 connection) with
the number 45050210410 (from outside Germany without the first 4), or by the ftp command (use: ftp 134.91.4.5). Under ftp, all programs can be downloaded with the commands "binary" (to set the transfer protocol to binary mode for program transfer) and  "get filename". The file transfer as as rapid as 0.5 - 1 Kbyte per second.

(3) Available through ASK, the Akademische Software Kooperation of the University of Karlsruhe, Germany. ASK is accessible via Internet (IP No. 192.67.194.33) or X.25 with the number 45050365010 (from outside Germany without the first 4). Login and password is ask. The installed Software Information System (ASK-SISY) provides a search and retrieval system and information on the programs. Programs can be downloaded directly or via electronic mail with ftp (IP No. see above).

(4) TAXACOM BBS, the Online Service for Systematic Botany and Phytogeography at the Clinton Herbarium (BUF). Taxacom is accessible by phone (2400/1200/300 baud, 8 data bits, 1 stop bit, no parity), available 24 hrs. without subscription. Dial 716-896-7581.. For details contact Dr. R.H. Zander, Buffalo Museum of Science, Humboldt Parkway, Buffalo, N.Y. 14211-1293, USA. Taxacom is also the host for Flora Online, the first electronical botanical journal.

(5) TAXACOM FTP, the same service as Taxacom BBS but accessible by Internet with the ftp command. Internet number is 35.8.196.1. Logon is "anonymous", password "ftp". Programs as well as data files are in various directories in the subdirectory /pub.




Other sources:

NISS, the National Information on Software & Services,  a British project similar to the German ASK (see under 3). NISS is accessible through ASK or via JANET. It includes a retrieval system for software. For biological software, it provides the  Resource Directory of the Computers in Teaching Initiative CTI) Centre for Biology, a compilation of more than 200 programs for all computer systems (incl. Apple Macintosh) of primarily commercial vendors. At present, this list does not include software for botanical apllications.



Bibliography on Computer Applications in Botany


Abbot, L.A., F.A. Bisby & D. Rogers 1985 Taxonomic analysis in biology. Computers, models and databases. Columbia University Press, London
Allkin, R. & F.A. Bisby 1984 Databases in Systematics Academic Press, London
Ammann, K. 1984 Dokumentation von Sammlungen und Literatur mit dem Mikrocomputer Diss. Bot. 72: 401-433
Baudoin, R., H. Bischler, S. Jovet-Ast & J.P. Hebrard 1984 Une banque de donnes phytoecologiques des hepatiques de la region mediteraneene (BRYOMED) Webbia 38: 385-396
Bisby, F.A. 1984 Automated taxonomic information systems. In: H. Heywood & D.M. Moore, Current concepts in plant taxonomy pp. 301-322. Academic Press, London
Brenan, J.P.M., R. Ross & J.T. Williams 1975 Computers in botanical collections Plenum Press, London
Callauch, R., Stallmann, G. 1987 Die Anfertigung pflanzensoziologischer Tabellen mit der neuen PST Version 2.0 Tuexenia 7: 497-498
Een, G. 1988. Computer assisted moss determination. Bryol. Times 48:4
Empain, A. 1988 Micro-computer aided description and comparison for bryophytes - a prototype. Monographs in Systematic Botany from the Missouri Botanical Garden 25:433-438.
Empain, A. 1986 Mesures semi-automatises au microscope. Bull. Soc. Roy. Bot. Belgique 118:93-99:
Empain, A. 1986: Etiquettes d'herbier: informatisation. Bull. Soc. Roy. Bot. Belgique 118:96-9Remarks:
Empain, A. 1987 A computerized workbench for the taxonomist. 1: Applications Bryological Times 41:1-2
Empain, A.M. 1988. A taxonomy-oriented computer language. PP. 329-335 in: J.M. Glime (ed.) Methods in Bryology. Nichinan.
Empain,A. 1987: Shape of moss leaves: a versatile method of description. Bulletin du Jardin Botanique National de Belgique 57:331-361.
Fink, H.G. & Kleifges, P. 1990 Die Datenbank der Florenkartierung: Struktur und Einsatzfhigkeit der Datenbestnde Stand 1980 fr das laufende Kartierungsvorhaben. Flor. Rundbr. 23: 150-159
Frahm, J.-P. 1988. Computer applications in bryology. Pp. 311-319 in: J.M.Glime (ed.), Methods in Bryology. Nichinan.
Frahm. J.-P. 1990 Scanning and digitizing of illustrations Bryol. Times 54: 8
Gibbs Russell, G.E. & P. Gonsalves 1984 PRECIS - A Curatorial and Biogeographic System. In: R. Allkin and F.A. Bisby (eds.) Databases in Systematics pp. 137-153. London
Heywood, V.H. 1984 Electronic Data Processing in Taxonomy and Systematics. In: R. Allkin and F.A.
Bisby (eds.), Databases in Systematics pp. 1-1Publication(s): London
Krauss, H. 1973 The information system design for the Flora North America Program Brittonia 25: 119-134
LaFarge-England, C. & B.J. O'Shea 1989 IAB Computer Workshop 24-27 February 1989, Mont Rigi, Belgium Bryol. Times 50: 1-3
Lightowlers, P. 1988. The Antarctic plant database and the BAS herbarium. Taxon 37:378-380.
Magill, R.E. 1982 Bryology and the desktop Computer Bryol. Times 13
Magill, R.E., G.E.Gibss Russell, J.W. Morris and P. Gonsalves 1984 PRECIS, the Botanical Research Institute herbarium data bank Bothalia 14: 481-495
May, R. 1990 Die Datenbank der Florenkartierung: Weiterentwicklung der Datenstrukturen -Einbindung von PCs in ein integriertes EDV Konzept. Flor. Rundbr. 23: 160-169
Michaelis, M., M. Michaelis & E. Hartmann 1988 Digital Image Analysis of developing Mosses pp. 337-342 in: J.M. Glime (ed.) Methods in Bryology, Nichinan
Morris, J.W. & H.F.Glen 1978 PRECIS, the National Herbarium of South Africa (PRE) computerized information system. Taxon 27: 449-462
O'Shea, B.J. 1988. An "expert system" approach to bryological identification. Pp. 321-326 in: J.M. Glime (ed.) Methods in Bryology. Nichinan.
O'Shea, B.J. 1990 Herbarium Management Bryological Times 54: 9-10
Pankhurst, R.J. (ed.) 1975 Biological identification with computers Academic Press, London
Peppler, C. 1988 TAB - Ein Computerprogramm fr die pflanzensoziologische Tabellenarbeit Tuexenia 8: 393-406
Platnick, N.I. 1989 An empirical comparison of microcomputer parsimony programs II. Cladistics 5:145-161
Rhoades, F.M. 1987: Synoptic keys for introducing students to lichens and bryophytes. Evansia 4:32.
Whittier, H.O., B.A. Whittier, H.A. Miller & H. Pringle 1988 Microcomputer Applications to Large Taxonomic and Biogeographic Data Files pp. 343-346 in: J.M. Glime (ed.) Methods in Bryology,Nichinan
Zander, R.H. & P.M.Eckel 1987: TAXACOM, an electronic bulletin board system. Bryological Times 42:1,4.



ALPHABETICAL INDEX OF PROGRAMS



Askataxa 4
Bacchus 13
Bids 2
Chorol 23
Cluster 15
Coenos 7
Coenosis 25
Curator 14
Decorana 9
Delta 5
DMap 11
Herb 27
Herbar 17
Herbarium Manager 10
Herblabel 29
Kartschl 3
Keyout 19
Lab 16
Labels3 32
Leafdemo 30
Loan 12
Mapping 21
Meka 20
MPSort 6
Pankey 1
Paup 22
PCTaxonUtilities 24
Phylip 28
PST 18
Sidgend2 31
Treesearch 8
Tropicos 26
Twinspan 9

SUBJECT INDEX







Cladistics 8,22,28
Ecology 7,9,25
Genetics 31
Herbarium Labels 16,17,29,32
Herbarium Management 10, 12, 13, 14, 26, 27
Identification 1,2,3,4,19,20,24
Mapping 11,21,23
Multivariate Analysis 9
Phenetics 9,15
Phylogeny 8,28
Plant Sociology 6,18
Systematics 9
Taxonomy 5,9,15,30

{SEITE|29}




-- 
Dr. A.J.Travis,                       |  JANET: <ajt at uk.ac.sari.rri>
Rowett Research Institute,            |  other: <ajt at rri.sari.ac.uk>
Greenburn Road, Bucksburn,            |  phone: +44 (0)224 712751
Aberdeen, AB2 9SB. UK.                |    fax: +44 (0)224 715349




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