		 






  Free Software in Molecular Biology
	for Macintosh and MS Windows computers
 
 
 
 
 
	 Don Gilbert
	 
	 
	 June 1998
		 
		 
		 
	 archive@bio.indiana.edu
	 Biology Department
	 Indiana University, Bloomington, IN 47405
	 
	 phone: 812.855.0587
	 fax: 812.855.6705
 
		 
 1. Introduction
		 You will find a large collection of free applications for molecular 
		 biology and chemistry through Internet servers and from other sources.	 Most of these 
		 are written by biologists, chemists, and software developers, sometimes as part of a 
		 university or government funded project, sometimes as an unfunded project.	 Some of 
		 these offer a single function useful to you, but one that may be found nowhere else.	 
		 What is free software for bioscientists,	 and especially where can you 
		 get it?	How do you set it up and use it?	What are some good programs, and what 
		 overall is available?	These are some of the questions you can find answers to in this 
		 review, which concentrates on software for molecular biology	 for the commonly used 
		 Macintosh and Microsoft (Wintel) operating systems.	
		 What you won't find answers to here include the many free programs that 
		 now run as an Internet service through your web browser.	 Neither listed are programs 
		 available mainly as source code	(not ready to run) or Unix programs,	nor the choices 
		 you have with commercial software,	 nor software for related areas of chemistry, 
		 medicine, population biology, ecology and others.
	 1.1	Free or commercial software?
		 Free data analysis software is common in the sciences, as the scientists 
		 in need of new analyses develop algorithms for it, then crystallize the algorithms as 
		 software.	Most of the basic biosequence analyses are scientist-developed, including 
		 FastA, BLAST, Clustal, MFOLD, PHYLIP, Paup, CAP, to name a few.	The source code of 
		 these is often shared freely.	But often these algorithm programs lack ease of use and 
		 integration with other functions.	Commercial software developers have incorporated 
		 such algorithms, along with their own, and added a much greater usability and 
		 integration, to allow you to analyze your data without spending oodles of time learning 
		 how to run the programs.
		 Besides adding integration and user-interface, companies add the great 
		 value of good documentation, telephone and other support for their wares.	When your 
		 funds permit, and a commercial package does what you need, it is usually a better 
		 choice than free software.	 Given market place realities, companies charge what seem 
		 large fees to you, but these fees are needed to cover the many aspects of publishing: 
		 advertising, technical support, software developers, and so forth.	 
		 For scientists with limited budgets, students and teachers, free 
		 software is often the only choice.	 You can also find unique programs that do things no 
		 commercial package does.		Another great advantage of free software is that it often 
		 includes source code you can use to modify and extend an analysis.	 
		 Today with the rapid growth in the fields of bioinformatics and 
		 biocomputing, more good programmers are developing software, many making it freely 
		 available.	 You will find more sophistication in attention to user interfaces and ease 
		 of your learning to use the software.	Still there is no common	means for funding 
		 development of free software: government agencies do not generally fund projects from 
		 individual research/programmers, the main source of many of the free software packages.	
		 The shareware concept of users paying for software they use has never worked well.		
		 For most scientific software, the potential market is so small that we see a strong 
		 distinction between expensive commercial packages and free software.
		 Usability of free programs is variable, and depends in part on your 
		 computer and needs.	 Be aware that	older programs may fail to work on new computers.	 
		 Tolerance for program flaws and limitations is generally needed, and self-reliance in 
		 learning how they work.	Often the authors either cannot be contacted, or do not have 
		 time to spare for supporting a product that they freely distribute.
	 1.2	Internet sources
		 Access to and use of the Internet has become so ubiquitous in our 
		 society, especially among scientists, that it is assumed	 you have or can get such 
		 access.	This wasn't true a few years back, but since the 1980s, free software for 
		 biosciences has been most widely available through the Internet, since distribution 
		 that way is free (from cost and time) to software authors.	 There are a few widely used 
		 archives of biosciences software, and today many authors prefer to provide their own 
		 network server to distribute software, as that is very easy to do.	 Archives which 
		 collect such software still play an important role in providing these collections, and 
		 in archiving them for years past when an author may be able to.	
		 Two commonly used archives of molecular biology software are IUBio 
		 Archive, at Indiana University, and the European Bioinformatics Institute (EBI) 
		 software archive.	Internet resource locators (URLs) for these are	 
			EBI at http://www.ebi.ac.uk/ or ftp://ftp.ebi.ac.uk/
		 The European Bioinformatics Institute, home to EMBL databank and others, 
		 and a home to a large molecular biology	software archive, including the very useful 
		 Bio Catalog of software (http://www.ebi.ac.uk/biocat/biocat.html).
			IUBio at http or ftp://iubio.bio.indiana.edu/
		 IUBio Archive is home to a large collection of biology software, and 
		 also provides services for keyword searching	 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 molecular biology 
		 software collection at IUBio is also mirrored (copied) to sites around the world, 
		 including the Finland, Sweden, Japan, United Kingdom, France, Spain, and Israel.	 See 
		 the following software listings section for URLs to these.
		 A few of many other Internet servers of note include
		 http://www.ncbi.nlm.nih.gov/ - home site for up-to-date access to Entrez 
		 software (databank lookups), Sequin for publishing your sequence in GenBank, Macaw 
		 (multiple alignment), and others.
		 http://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 their search launcher program (a Perl script that is usable on 
		 Macintosh and Wintel systems) for batch access to this valuable resource.
		 http://expasy.hcuge.ch/ - home of SwissProt, ProSite and home to a 
		 collection of useful database analyses functions, especially for protein data.
	 1.3	Fetching software
		 File 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 a better 
		 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.	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.
		 Generally software is stored and transferred to you in encoded formats 
		 from archives.	 Most current fetching software, like Fetch and Netscape, will decode 
		 this automatically for you.	However, other software sometimes is used or needed for 
		 decoding.	General Internet software packages and servers will get you started on what 
		 is needed.	 If in doubt, your local library or bookstore will have a few shelves full 
		 of books on using Internet services and general software archives.	 
		 The main trick in fetching software these days is knowing where to look.	 
		 Besides this review, you can make use of web links made by others, perhaps with better 
		 perspective than this author.	See also the common Internet search services, like Yahoo 
		 (http://www.yahoo.com/), AltaVista (http://www.altavista.digital.com/),	Lycos 
		 (http://www.lycos.com/) or others.
		 Keep in mind that software is updated; if the version you try fails in 
		 some way, a newer version may be available now or soon.	The author's preferred or home 
		 server is the best place to check for updates, as archive servers don't always have the 
		 current release.
	 1.4	Setup and use
		 Once on your computer, the steps of installing and configuring free 
		 software range from easy to trying.	 Instructions are usually included, but are not 
		 always detailed enough, or cover all the range of problems one can run into.		Special 
		 installing software is common with commercial software, but not with the free variety.	 
		 Report problems you have to the author, and suggestions for improving 
		 the software.	Asking the frequently overworked authors for help with installation 
		 isn't always good solution though, so attention to their pre-written installation 
		 directions is essential. 
		 Special kinds of software, especially those written for Java or Perl, 
		 will require that you also fetch and install other free, general software to use.	In 
		 the case of Java, this is becoming less a problem as new MacOS and UNIX	systems are 
		 shipping with a Java runtime as part of the system.
	 1.5	Multi-platform software
		 By 1998 counts of Internet browser contacts at IUBio and other biology 
		 web servers, from 30% to 50% of 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 have access to multiple 
		 operating systems, depending on what software runs on.		Also of help, there are 
		 commercial emulator programs that allows one to run most MS Windows and MSDOS software 
		 on Macintoshes, 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 who develop scientific applications - one hopes a program can be 
		 used by anyone needing it, on any computer system.		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 expend effort that is	 not always successful (e.g., WordPerfect on UNIX 
		 pales compared to the MacOS or Wintel versions).
		 With the case of graphical interface software that most of us expect 
		 today, multi-platform programs	 may not look quite right on your particular system, 
		 even though they operate as intended.	In the more common case of software with no 
		 graphical interface, you may need to devote extra time to learning its command-line or 
		 menu driven syntax.
		 The new Java development system born at Sun Microsystems 
		 (http://www.javasoft.com), now is providing a means for developing useful software that 
		 works well on common systems, albeit at present Java software is frequently slower than 
		 its counterpart written in C++, C or other languages.	We may expect to see much more 
		 software in biocomputing written in Java in coming years.	See for instance the new 
		 sequencing analysis package from Licor (www.licor.com).
	 1.6	Client-Server biosequence software
		 There 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 basis of a client-server design for 
		 software.	Simple examples of this are web interfaces that abound now for various data 
		 analyses.	
		 This author's own work-in-progress SeqPup takes this approach:	 it 
		 allows you to use the analysis software 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 editing sequences, basic 
		 manipulations and alignments, and sophisticated display and output options.	It also 
		 links to analysis "engines" in a way you can configure to your taste.	 These analysis 
		 programs encode the complex 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 to organize 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.
		 Peter 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 a command-line interface.	 EMBOSS will 
		 include various sequence analysis topics, and will include a major effort to provide 
		 easy integration of other public domain packages.	Analyses include rapid database 
		 searching with sequence patterns, and for sequence overlaps,	 simple and 
		 species-specific repeat identification, nucleotide sequence pattern analysis, codon 
		 usage analysis for small genomes, gene identification tools for genomic sequencing, 
		 rapid identification of sequence patterns in large scale sequence sets, protein motif 
		 identification, and presentation tools for publication.
		 These could be the basic analysis engines for sequence analysis, and 
		 some client program with a good user interface, perhaps like SeqPup, Java applets, or 
		 web forms, can be the program you use to run the analyses. 
 2.	 Free software highlights
	 2.1	Clustal sequence alignment
		 Clustal 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 many nucleotide or amino acid sequences is 
		 now an essential tool in molecular biology.	Multiple alignments are used to find 
		 diagnostic patterns to characterize protein families; to detect or demonstrate homology 
		 between new sequences and existing families of sequences; to help predict the secondary 
		 and tertiary structures of new sequences; to suggest oligonucleotide primers for PCR; 
		 as an essential prelude to molecular evolutionary analysis. The Clustal program fits 
		 this need very well.	 It is available at ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW and 
		 at EBI and IUBio archives.	 There is a companion program ClustalX which provides a 
		 graphic interface to Clustal, and Clustal can be used from other sequence editors such 
		 as SeqPup.
	 2.2	Entrez to search genome data
		 The 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 be obtained from http or 
		 ftp://ncbi.nlm.nih.gov/.		Entrez runs on a variety of computer systems.	 One big 
		 advantage of Entrez is the inclusion of a subset of MEDLINE,	 which covers the 
		 abstracts of entries submitted to the sequence databases. The WWW service of NCBI also 
		 offers an Entrez type of capability through your web browser.		The program source for 
		 Entrez developed at NCBI has been instrumental in providing a software framework for 
		 other biosciences applications, including a version of SeqPup and Clustal-X.
	 2.3	NIH Image for image analysis
		 A 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 user defined region of interest.	It 
		 also performs automated particle analysis and can be used to measure path lengths 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 at 
		 ftp://zippy.nimh.nih.gov/pub/nih-image/, or http://rsb.info.nih.gov/nih-image/.	 There 
		 is now a version for MS Windows, from http://www.scioncorp.com/ .
	 2.4	PHYLIP for phylogeny analyses
		 The widely used Phylogeny Inference Package, PHYLIP, from Joseph 
		 Felsenstein, is a package of programs for inferring phylogenies (evolutionary trees), 
		 and written to work on as many different of computer systems as possible.	It includes 
		 analyses of DNA and protein sequences, restriction sites, distance matrices and gene 
		 frequencies, quantitative and discrete characters, and plotting of evolutionary trees.		
		 Algorithms used include parsimony, maximum likelihood, neighbor joining and several 
		 others. Many options for precise control of the analyses are available.	The home for 
		 PHYLIP is at http or ftp://evolution.genetics.washington.edu/. 
	 2.5	RasMol for molecular modeling
		 RasMol 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 quality images.	 RasMol runs on all 
		 common computer systems.	 The program reads in	 molecule	 co-ordinates and 
		 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/
	 2.6	SeqPup for sequence editing
		 SeqPup, and its predecessor SeqApp, are biological sequence editor and 
		 analysis programs.	 They includes 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 sequence file formats, pretty print of alignments and 
		 sequences with boxed and shaded regions, sequence feature editing, manipulation and 
		 marking in prints, consensus, reverse-complement, distance/similarity, translate DNA 
		 to/from protein.	 Print file formats include PICT, Postscript and GIF.
		 User-definable links to external analysis programs, including ClustalW 
		 multiple alignment, CAP contig assembly, tacg restriction maps, fastDNAml phylogenetic 
		 analysis are included, and others can be added by you.	 One can use these running on 
		 your own computer or on an Internet server computer, using a new CORBA protocol 
		 (www.corba.org).		Internet sequence analysis services include fetching sequences using 
		 SRS keyword search, and performing NCBI-BLAST similarity searches.
		 The home for SeqPup is http://iubio.bio.indiana.edu/soft/molbio/seqpup/.	 
		 Note that this application is a work in progress; it has bugs.	 SeqApp is the 
		 Macintosh-only predecessor to SeqPup.	Many folks find this currently a more useful 
		 program than SeqPup.	 It is faster, but lacks newer features of SeqPup.
 3.	 Software use issues
	 3.1	Copyrighted versus public domain
		 Most 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 software in commercial packages or 
		 other uses that make money require consent from the author.	 Many of the free software 
		 programs come with source code, so you can modify and extend it.	 This is a great boon 
		 to let sophisticated users do a needed analysis, but keep in mind use of such in a 
		 commercial product isn't allowed.	 If the author explicitly places his work in the 
		 public domain, s/he retains no control, and it can be used in commercial applications.	 
	 3.2	Citing software publications
		 Publicly available software is a publication, and free software that you 
		 use should be treated with consideration that you give other publications used in your 
		 research.	While some free software has a companion paper publication to cite, some 
		 does not.	It is usual practice to cite a software publication with its Internet URL in 
		 place of the journal/volume portion, e.g., 
					Felsenstein, 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, July 1996.	 <news://4rb7hr$6rc@usenet.ucs.indiana.edu>		See 
						also ftp://iubio.bio.indiana.edu /molbio/seqpup/
		 Some 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.
 4.	 Acknowledgments
		 The many developers of free software for biosciences, some of them 
		 mentioned herein, are the real authors of this document.	 If you use their software, 
		 please let them know you find it useful.	 Often one program builds 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,	 
		 Peter Markiewicz, Thure Etzold, Xiaoqiu Huang, Des Higgins, Harry Mangalam, Jim Brown, 
		 Bill Pearson,	and many others who provided their sweat and ideas to help make his own 
		 works useful.	 The many users of software who offer suggestions, criticisms and 
		 insights on how software should work, also contribute enormously to making free 
		 software better for all to use.	 The former GenBank home at Intelligenetics in the 
		 1980s held an archive for free molecular biology software, to which many of us owe 
		 thanks for their pioneer efforts.
		 
		 
 5.	 Software listings
		 This 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)
		 Software archive abbreviations:
			ebi -	 ftp://ftp.ebi.ac.uk/pub/software/	or	
		 http://www.ebi.ac.uk/software/software.html
			iubio -	 ftp://iubio.bio.indiana.edu/molbio/	or	
		 http://iubio.bio.indiana.edu/soft/molbio/
			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
		 Some Email addresses and home URLs may be out of date.		Unless 
		 otherwise indicated, all software listed is copyrighted by the author, and is available 
		 free for non-commercial use.	 Specific copyright restrictions should be noted.	 Some of 
		 this software is shareware, the author requesting a fee for use.
		 
		 
		 ABaCUS M, W, O
		 ABaCUS is a no-frills program to investigate the significance of the 
		 putative correspondence between exons and units of protein structure.
		 Author:	Arlin Stoltzfus, arlin@is.dal.ca
		 Archive: iubio/evolve/abacus/
		 ADE-4	M
		 ADE-4 is a multivariate analysis and graphical display software package 
		 for Macintosh micro-computers.
		 Author:	Olivier J.M. and others, 
							Jean-Michel.Olivier@biomserv.univ-lyon1.fr
		 Home:	ftp://biom3.univ-lyon1.fr/pub/mac/ADE/ADE4, 
							http://biomserv.univ-lyon1.fr/ADE-4.html
		 Amplify	 M
		 This Macintosh software is for use in designing, analyzing, and 
		 simulating experiments involving the polymerase chain reaction (PCR).	Amplify will 
		 search a target sequence for near matches and display the results of using various 
		 primers.	 It can check oligos for matching sequence and for internal repeats.
		 Author:	Bill Engels, WREngels@macc.wisc.edu
		 Archive: iubio/mac/amplify*,	 ebi/mac/
		 AnalyzeSignalase		 M
		 A Macintosh program for applying the algorithm of von Heijne to the 
		 prediction and analysis of mammalian signal sequences.	 It uses a weight- matrix method 
		 to try to predict the site at which signal peptides in secretory peptides are cut off 
		 by the signal peptidase.
		 Author:	Ned Mantei
		 Archive: iubio/mac/analyze-signalase*
		 Ancestor W
		 Ancestor is designed to infer ancestral amino acid sequences from a set 
		 of homologous amino acid sequences whose phylogenetic relationships
		 are known. 
		 Author:	Jianzhi Zhang, zhang@imeg.bio.psu.edu
		 Archive: iubio/ibmpc/ancestor*
		 Annhyb W
		 Annhyb is a little program for Windows 95 that is able to calculate 
		 various DNA sequence (degenerated or not) parameters. 
		 Author:	O. Friard & G. Stefanuto, friard@ba.cnr.it
		 Home:	http://area.ba.cnr.it/~e105of01/annhyb221.zip+
		 Antheprot	W, O
		 ANalyze THE PROTeins (ANTHEPROT) is a package includes study of 
		 physico-chemical properties: hydrophobicity, antigenicity, flexibility, solvent 
		 accessibility, amphiphilicity;	 secondary structure prediction: Chou & Fasman, Garnier, 
		 Gibrat, Deleage, Levin;	prediction of transmembranous regions & of structural domains;	
		 multiple alignment;	search for biological sites using PROSITE, and PATMAT; search for 
		 homologous protein using FASTA; identity level between several sequences.	Look and 
		 handle protein structures from PDB.
		 Author:	G. Deleage, deleage@ibcp.fr &	 C. Geourjon, geourjon@ibcp.fr 
		 Home:	http, ftp://www.ibcp.fr/
		 Archive: iubio/ibmpc/antheprot*
		 Automatic-BLAST	M
		 This is an AppleScript that automatically sends sequences by email to 
		 the BLAST server at ncbi.nlm.nih.gov at prescribed times, daily or weekly. The script 
		 uses the scriptable email program Eudora.
		 Author:	Brian Osborne, bosborne@nature.berkeley.edu
		 Home:	http://pgebaker4.pw.usda.­gov/bio/bio.html
		 Archive:		iubio/mac/automatic-blast.*
		 BCM Search Launcher	M, W, O (Perl)
		 The 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-entry for	 related searches.	There is a 
		 batch client interface for Unix and Macintosh computers that allows multiple input 
		 sequences to be automatically searched as a background task, with the results returned 
		 as individual HTML documents. Requires Perl.
		 Author:	Randall F. Smith et al.
		 Home:	http://gc.bcm.tmc.edu:8088/search-launcher/launcher.html
		 BufferStack	 M
		 Given the appropriate information, the BufferStack will construct	a 
		 complete recipe for a buffer that is defined in terms of both	pH and ionic strength, 
		 at the temperature of use. 
		 Author:	Rob Beynon
		 Archive: iubio/mac/buffer*, ebi/mac/bufstack*
		 Cabuffer W
		 This program allows you to calculate the concentrations of all ionic 
		 species present in a mixture of up to four 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. 
		 Author:	Jochen Kleinschmidt, kleinschmidt@mcclb0.med.nyu.edu
		 Archive: iubio/ibmpc/cabuf*
		 CAIC		M
		 CAIC, Comparative Analysis by Independent Contrasts, computes 
		 phylogenetically independent contrasts from comparative data, allowing valid	 
		 statistical testing of adaptational hypotheses.	The manual	gives guidance on testing 
		 hypotheses of correlated evolution among traits, rate variation among traits or taxa, 
		 and grade	shifts. 
		 Author:	Andy Purvis & Andrew Rambaut, Andrew.Rambaut@zoology.ox.ac.uk
		 Home:	http://evolve.zps.ox.ac.uk/CAIC/CAIC.html
		 CAP	M, W, O
		 Contig Assembly Program based on sensitive detection of fragment 
		 overlaps. C source, command-line program, can be used from SeqPup, others.
		 Author:	Xiaoqiu Huang, huang@cs.mtu.edu
		 Home:	ftp://cs.mtu.edu/pub/huang/
		 Archive: iubio/align/cap*
		 CGR	M
		 A HyperCard stack for presenting nucleotide sequence data using Chaos 
		 Game Representation.
		 Author:	Heikki Lehva, lehvaslaiho@cc.helsinki.fi
		 Archive::	iubio/mac/cgr*, ebi/mac/cgr*
		 Clustal W	M, W, O
		 A 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, position-specific gap penalties and 
		 weight matrix choice. Nucleic Acids Res. 22:4673-4680(1994).
		 Author:	D. Higgins et al.
		 Home:	ftp://ftp-igbmc.u-strasbg.fr/pub/Clustal*
		 Archive: ebi/mac/clustalw*,	ebi/dos/clustalw*,	iubio/align/clustal*
		 ClustalX M, W, O
		 ClustalX is a graphic interface for the ClustalW alignment program. The 
		 sequence alignment is displayed in a window on the screen, with pull-down menus. 
		 Author:	Thompson J.D et al., julie@igbmc.u-strasbg.fr
		 Home:	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX
		 Codon Frequency Analyzer W
		 This program helps to identify coding regions of DNA by comparing the 
		 codon frequencies in known coding regions with a sequence of DNA, the coding regions of 
		 which are unknown. The program will work with any organism.
		 Author:	Ballyclaire Analysis
		 Archive: iubio/ibmpc/codon*
		 CodonBiasIndex M
		 The codon bias index is a statistic created by Bennetzen and Hall to 
		 quantify the extent to which more frequently used codons are used in preference to less 
		 frequently used codons. 
		 Author:	Tom Ritch, ritch@seas.ucla.edu
		 Archive: iubio/mac/codonbioasindex*
		 Comap	W
		 A program for helping with the construction of
		 restriction maps of small DNA fragment from digestion data. The program 
		 works under a graphical user interface.
		 Author:	Kay Hofmann, khofmann@cipvax.biolan.uni-koeln.de
		 Archive: iubio/ibmpc/codon*, ebi/dos/
		 ConsInspector	M, W, O
		 ConsInspector uses a precompiled library of extended weight matrix 
		 descriptions (consensus profiles) of transcription factor binding sites to scan nucleic 
		 acid sequences for matches to these sites.
		 Author:	K. Frech, et al. frech@gsf.de
		 Home:	ftp://ariane.gsf.de/pub/
		 Covariation	M
		 A Hypercard stack for phylogenetic comparative analysis of aligned RNA 
		 sequences.
		 Author:	James W. Brown, jwbrown@mbio.ncsu.edu
		 Archive: iubio/mac/covariation*, ebi/mac
		 CPrimer	M
		 CPrimer evaluates oligonucleotides as possible PCR primers.	It shows 
		 melting points, interfering structures, and can search for optimum amplification pairs.
		 Author:	Greg Bristol, gbristol@ucla.edu
		 Archive: iubio/mac/cprimer*
		 DCSE		W, O
		 Dedicated Comparative Sequence Editor is a multiple alignment editor. It 
		 can be used to edit protein, DNA or RNA alignments. The structure of the molecules can 
		 be incorporated in the alignment. It offers lots of features such as color display of 
		 characters and structure, automatic alignment relative to sequences already aligned 
		 with others, sequence grouping, sequence or pattern searching, marker system, checking 
		 of incorporated RNA structure, on-line hypertext help, macros, and a lot more.
		 Author:	Peter De Rijk, derijkp@reks.uia.ac.be
		 Home:	http://www-rrna.uia.ac.be/~peter/dcse
		 Archive: ebi/dos/dcse
		 Digest W 
		 Digest scans DNA sequence files for restriction sites.	 It prompts the 
		 user to specify which enzymes to cut with, and if they are in the enzyme
		 database, it writes out the positions of all the cuts and sorts the 
		 fragments by size.
		 Author:	Ramin Nakisa, ramin@ic.ac.uk
		 Archive: iubio/ibmpc/digest*, ebi/dos/digest*
		 Digispeak	M
		 A program for reading sequencing gels with the aid of a Graf-Bar or 
		 similar sonic digitizer. 
		 Author:	Ned Mantei, bcmantei@aeolus.vmsmail.ethz.ch
		 Archive: iubio/mac/digispeak*, ebi/mac/
		 Dispan W
		 DISPAN (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 phylogenetic trees and does 
		 bootstrap tests.
		 Author:	Tatsuya Ota, imeg@psuvm.psu.edu
		 Archive: iubio/ibmpc/dispan*
		 DNA Runs M
		 DNA Runs is a program for performing a significance test of the number 
		 of runs in DNA sequence polymorphism and divergence data.	
		 Author:	John H. McDonald, mcdonald@udel.edu
		 Home:	http://udel.edu/~mcdonald/
		 Archive: iubio/mac/dna-runs*
		 DNA Slider M
		 DNA Slider is a program for performing a significance test of 
		 heterogeneity in the ratio of polymorphic sites to fixed differences in DNA sequence 
		 data. 
		 Author:	John H. McDonald, mcdonald@udel.edu
		 Home:	http://udel.edu/~mcdonald/
		 Archive: iubio/mac/dna-slider*
		 DNA Stacks M
		 DNA Stacks is a software package of HyperCard stacks providing utilities 
		 for viewing and manipulating molecular data. DNA Translator includes a gene mapping 
		 facility, draws and displays 2 linearized gene maps for comparison.	Aligner is a stack 
		 for editing and display of multiple alignments.	Codon Usage displays codon and amino 
		 acid usage data for a variety of organisms and organelles.
		 Author:	D. J. Eernisse, DEernisse@fullerton.edu
		 Home:	http://biology.fullerton.edu/people/faculty/doug-eernisse
		 Archive: iubio/mac/dnastacks*, ebi/mac/
		 Dna Workbench	M, W, O (Perl)
		 A program for sequence searching and manipulation.	 It offers powerful 
		 and fast searches on Genbank and other databases. Client-server access to remote 
		 databases and programs. Its many sequence manipulation functions include calculating 
		 the reverse complement, displaying reading frames and nucleotide to protein 
		 translations, editing, searching for restriction enzyme sites, searching for human 
		 repeat or vector in a sequence, comparing a sequence against a library or a user file, 
		 searching for a regular expression in a sequence.	It requires Perl.
		 Author:	James Tisdall, tisdall@cbil.humgen.upenn.edu
		 Home:	ftp://cbil.humgen.upenn.edu/pub/dnaworkbench
		 DNAdraw	M
		 DNAdraw is a program designed for preparing DNA and protein sequences 
		 for publication.	 A large selection of highlighting options is available.	It has 
		 special features for formatting raw data into a style commonly used for publication, 
		 and for doing automatic highlighting of aligned sequences.
		 Author:	Marvin Shapiro, mbs@kias.com
		 Archive: iubio/mac/dnadraw*
		 DNAfrag	W
		 This program is used in restriction mapping of DNA or sizing of proteins 
		 from gels.	 It calculates the size of restriction fragments or peptide bands if 
		 standards are run on the same gel, and a standard curve of the standard bands using 
		 their mobilities.
		 Author:	John Nash, Nash@biologysx.lan.nrc.ca
		 Archive: iubio/ibmpc/dnafrag*, ebi/dos/dfrag*
		 DnaSP	W
		 DnaSP	is a package for Windows that performs extensive population 
		 genetics analysis on DNA data, for hundreds of sequences of thousands of bases.	It 
		 estimates several measures of polymorphism within and between populations, linkage 
		 disequilibrium, recombination, gene flow, gene conversion, and neutrality.	 DnaSP can 
		 do analyses by a sliding window method, and will make graphic representations. 
		 Author:	Julio Rozas & Ricardo Rozas, julio@porthos.bio.ub.es
		 Home:	http://www.bio.ub.es/~julio/DnaSP.html
		 Archive: ebi/dos/dnasp
		 Dotplot	W
		 A dotplot program for MS-DOS.
		 Author:	Ramin Nakisa, ramin@ic.ac.uk
		 Archive: iubio/ibmpc/dotplot*, dprel3*, ebi/dos/dotplot*
		 Dotty Plotter	M
		 Dotty Plotter is a tool for drawing dot matrix comparisons of sequences 
		 in molecular biology.	Dot plots are used to view all areas of homology between two 
		 nucleic acid or protein sequences. 
		 Author:	D. Gilbert, software@bio.indiana.edu
		 Home:	iubio/mac/dottyplot*, ebi/mac/
		 Double Digester	M, O
		 This is a program designed	 to help researchers in molecular biology	 
		 assemble restriction maps of DNA using data	from double digest experiments.
		 Author:	L. Wright, wright-lawrence@yale.edu
		 Archive: iubio/restrict-enz/, ebi/mac/
		 dPrimer	M
		 This Macintosh software is for use in calculating Tm values for	
		 degenerate primer. 
		 Author:	Haoyuan Chen, hchen@bimcore.emory.edu
		 Archive: iubio/mac/dprimer*
		 EditView M
		 DNA Sequence Viewer for ABI Sequencer trace data.	EditView is a 
		 software application that allows you to view and print analyzed sample files containing 
		 sequence data from an ABI PRISM Genetic Analyzer. 
		 Author:	EditView@perkin-elmer.com
		 Home:	
							ftp://ftp.abd.perkin-elmer.com/pub/public/Sequencing/EditView/EditView1.0.1.sea.hqx
		 Archive: iubio/mac/editview*
		 Entrez M, W, O
		 Entrez is a molecular sequence retrieval	 system developed at the 
		 National Center for	Biotechnology Information (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	a sequence-associated 
		 subset of MEDLINE. 
		 Author:	various at NCBI
		 Home:	ftp://ncbi.nlm.nih.gov/entrez/
		 Enzyme Kinetics	M
		 Enzyme Kinetics is a Hypercard stack for Macintosh computers. It 
		 calculates and plots the biochemical values for the kinetics of enzyme-catalyzed 
		 reactions. 
		 Author:	D. Gilbert, software@bio.indiana.edu
		 Archive: iubio/mac/enzymekinetic*, ebi/mac/enzymekin* 
		 Esee		W
		 Eyeball SEquence Editor, for MS DOS.
		 Author:	Eric L. Cabot,	cabot@gcg.com
		 Archive: iubio/ibmpc/esee*
		 FastA	M, W, O
		 The FASTA sequence comparison programs,	improved versions of the FASTP 
		 program, originally described in Science (Lipman and Pearson, (1985) Science 
		 227:1435-1441)
		 Author:	Bill Pearson, wrp@virginia.edu
		 Home:	ftp://ftp.virginia.edu/pub/fasta/
		 Archive: iubio/search/fasta*
		 fastDNAml	M, W, O
		 fastDNAml is a faster version of Joseph Felsenstein's DNAML (part of 
		 PHYLIP).	 Users should consult the documentation for DNAML before using this program.
		 Author:	Gary J. Olsen et al., gary@phylo.life.uiuc.edu
		 Archive: iubio/evolve/fastdna*
		 FoldIt M
		 FoldIt (light) is a molecular modelling program to visualize and 
		 manipulate proteins.	 It has an integrated environment in which statistical analysis as 
		 well 3D observations can be realized on PDB files.	 It can analyze 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. 
		 Author:	Jean-Claude JESIOR, jean-claude.jesior@imag.fr
		 Home:	ftp://ftp.imag.fr/pub/TIMC/FoldIt.html
		 Archive: iubio/mac/foldit*, ebi/mac/
		 GCUA M, O
		 General Codon Usage Analysis.	 This program is designed to calculate 
		 various parameters that might be relevant in accessing the codon usage patterns of a 
		 group of genes.	The user can look at codon usage (or any 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 usage frequency, RSCU values, amino acid frequency data, base composition; 
		 distances between genes; ability to analyse complete prokaryotic genomes .
		 Author:	James O. McInerney, J.mcinerney@nhm.ac.uk
		 Home:	ftp://ftp.nhm.ac.uk/pub/gcua/
		 Archive: iubio/mac/gcua*
		 Gel	M, W
		 An application to calculate the size of DNA	fragment in an	agarose 
		 gel.
		 Author:	Jean-Michel Lacroix, lacroix@medac.med.utoronto.ca
		 Archive: iubio/mac/gel-jml, iubio/ibmpc/gel-jml, ebi/mac/gel-jml, 
							ebi/dos/gel-jml
		 Gel	W
		 GEL takes a set of standard DNA fragment sizes and mobilities and	
		 predicts the sizes of unknown fragments, using a least squares fit to the relationship 
		 of mobility and fragment length.
		 Author:	John R. Thompson
		 Archive: iubio/ibmpc/gel*, ebi/dos/gel/
		 Gel Frag Sizer M
		 Gel Frag Sizer is a HyperCard stack which calculates restriction 
		 fragment sizes from their mobilities.	Two methods for estimating sizes are provided: 
		 the local reciprocal method of Elder & Southern or the cubic spline method.
		 Author:	D. Gilbert, software@bio.indiana.edu
		 Home:	iubio/mac/gelfragsizer.*
			Archive:	ebi/mac/
		 Gel Manager	W
		 Gel Manager is a user friendly program which runs in MS Windows. It 
		 includes techniques of image processing 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 including genetic relationships, 
		 taxonomy and classification , epidemiology, etc.
		 Author:	Carlos Vaquerizo, Joaquin Dopazo, dopazo@samba.cnb.uam.es
		 Home:	ftp://ftp.cnb.uam.es/software/molbiol/gel_man
		 GeneDoc	W
		 GeneDoc is a full featured multiple sequence alignment editor and 
		 shading utility. It is intended to help you bring your genetics research work to 
		 publication with shading,	page and font layout features.	
		 Author:	Karl Nicholas, ketchup@cris.com
		 Home:	http://www.cris.com/~ketchup/genedoc.shtml
		 Archive: iubio/ibmpc/genedoc*
		 GeneMaster W
		 A 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.
		 Author:	Shawn Abigail, ad873@freenet.carleton.ca
		 Archive: iubio/ibmpc/genemast*
		 GeneTree M, W
		 GeneTree is a program for comparing gene and species trees using 
		 reconciled trees. The program can compute	the cost of embedding a gene tree within a 
		 species tree, visually display the location and number of gene duplications and losses, 
		 and search for optimal species	 trees.
		 Author:	Roderic D. M. Page, r.page@bio.gla.ac.uk
		 Home:	http://taxonomy.zoology.gla.ac.uk/rod/genetree/
		 Gepasi W
		 Gepasi 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 compartments of different volumes.	 
		 Results can be plotted in 2D and 3D graphs directly from the program. Steady states are 
		 analysed with metabolic control analysis and linear stability analysis.
		 Author:	Pedro Mendes, prm@aber.ac.uk
		 Home:	http://gepasi.dbs.aber.ac.uk/softw/gepasi.html
		 Archive: ebi/dos/
		 HDProbe	M
		 HDProbe 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 their orientation in a heteroduplex 
		 molecule. 
		 Author:	Marvin Shapiro, mbs@pa.net
		 Home:	iubio/mac/hdprobe.*
		 HelixVu	W
		 HelixVu illustrates an 80 bp region of DNA as a helix with the sequence 
		 listing printed above the helix diagram.	 This view is useful to see the spatial 
		 relationship between DNA modifications.	
		 Author:	Richard Seyler
		 Archive: iubio/ibmpc/helixvu*
		 Hyper	W
		 Hyper is a program for the analysis of enzyme kinetic data under MS 
		 Windows.	 Enzyme kinetic data are subjected to non-linear regression and the results 
		 displayed in five standard graphical forms and printed.
		 Author:	J S Eastery, jse@liverpool.ac.uk
		 Archive: iubio/ibmpc/hyper*
		 HyperPCR M
		 A HyperCard stack that calculates the optimal annealing temp. of a PCR 
		 reaction according to the algorithm of Rychlik.
		 Author:	Brian Osborne, bosborne@violet.berkeley.edu
		 Archive: iubio/mac/hyperpcr*, ebi/mac/
		 Intron Analyzer	W
		 There	are	 basic differences in	 the base composition of introns from 
		 animals and plants, and this program will examine introns to find regularities.	From a 
		 given list of introns you can explore by aligning them either at the 5' or at the 3' 
		 end, or study the adjoining exon-parts. The program will	 build	a consensus-sequence 
		 which shows the most frequent base in each	 position, including a graphic plot.
		 Author:	Michael Liss, LISS@alf1.ngate.uni-regensburg.de
		 Archive: iubio/ibmpc/intron-analyzer*, ebi/dos/intana*
		 Lalnview M, W, O
		 LalnView is a graphical program for visualizing local	alignments 
		 between two sequences.	 Sequences are represented by colored rectangles to give an 
		 overall picture of their similarities. It is able to display sequence features (active 
		 site, domain,	motif, propeptide, etc.) along the alignment.	 LalnView is a useful tool 
		 for analysing	pairwise alignments and for making the link	 between sequence homology 
		 and what is known about its structure or function.
		 Author:	Laurent Duret, duret@dim.hcuge.ch
		 Home:	ftp://expasy.hcuge.ch/pub/lalnview
		 Lines&Kinetics M
		 A graphic way to calculate linear regressions with normal	or 
		 logarithmic data, the doubling time of a microbial culture, and the kinetic parameters 
		 for an enzyme reaction. 
		 Author:	Manuel G. Claros, claros@uma.es
		 Home:	http://www.ie.embnet.org/embnet.news/vol5_1/kinetics.html
		 Archive: iubio/mac/lines-kinetics*
		 Linkage-1	M
		 designed to aid the geneticist in the detection and estimation of 
		 linkage in segregating progenies.
		 Author:	Karl A. Suiter, ksuiter@acpub.duke.edu
		 Home:	iubio/mac/linkage1*
		 Lintr	W, O
		 These programs are for testing the molecular clock on a given topology 
		 of a phylogenetic tree and making linearized trees, using nucleotide or amino acid 
		 sequences.
		 Author:	Naoko Takezaki, ntakezak@lab.nig.ac.jp
		 Archive: iubio/evolve/lintr/
		 LoopDLoop	M, W, O (Java)
		 loopDloop is a tool for drawing and editing RNA secondary	structures in 
		 molecular biology.	 A MacOS specific and Java version are available.		Mulfold will 
		 generate RNA foldings for display by loopDloop.	A related program, LoopViewer, lacks 
		 the editing features but is simpler to use. 
		 Author:	D. Gilbert, software@bio.indiana.edu
		 Home:	iubio/loopdloop/
		 Archive: ebi/mac/loop*
		 MACAW	M, W
		 Multiple 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 a multiple alignment.	 It includes 
		 sequence alignment search, editing and display. It is a very nice program according to 
		 many, allowing one to look for blocks of homology in sequences.
		 Author:	Greg Schuler &	Stephen Altschul, schuler@ncbi.nlm.nih.gov
		 Home:	ftp://ncbi.nlm.nih.gov/pub/macaw/
		 Archive: iubio/ncbi/macaw/, ebi/dos/macaw*
		 MacBoxshade	M, O
		 A program for creating good-looking printouts from multiple aligned 
		 protein or DNA sequences. The program does no alignment by itself, it uses files from a 
		 multiple alignment program. Output can be PostScript, EPSF, PICT, RTF or ASCII text. 
		 Identical and similar residues in the multiple-alignment are represented by different 
		 colors or shadings. There are many options of shading, sequence numbering, consensus 
		 output and so on.	
		 Author:	Michael D. Baron,	 michael.baron@bbsrc.ac.uk (macos),	 Kay 
							Hofmann (original)
		 Home:	ftp://ulrec3.unil.ch/pub/boxshade/macboxshade
		 Archive: iubio/mac/macboxshade*
		 MacPattern M
		 MacPattern is a Macintosh application for protein pattern searches 
		 (using PROSITE) and block profile searches (using BLOCKS). MacPattern assists in 
		 finding putative functions for new protein sequences by supporting pattern searches 
		 using the PROSITE database, block searches using the BLOCKS database, and statistical 
		 analyses (maximal segment score analysis and Eguchi-Seto method). 
		 Author:	Rainer Fuchs, rainer_fuchs@glaxo.com
		 Archive: iubio/mac/macpattern*, ebi/mac
		 MacPlasmap M
		 If your study or research involves preparation of circular plasmid	 
		 maps, you will find MacPlasmap an indispensable tool to have. It	 draws, stores, and 
		 prints high-quality circular plasmid maps with	 the data you specify.	
		 Author:	Jingdong Liu
		 Archive: iubio/mac/macplasmap*, ebi/mac/
		 MacProt	M
		 MacProt is a of a set of programs for analyzing protein	sequences for 
		 secondary structure, chain flexibility, hydropathy,	helical wheels, and so on. 
		 Author:	Peter Markiewicz
		 Archive: iubio/mac/plota/, ebi/mac/plota_*
		 MacStripe	M
		 MacStripe 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 the sequence of their protein. 
		 With a full Macintosh interface, the results of analyses (raw data or publication 
		 quality plots) can easily be exported to other software. MacStripe uses the algorithm 
		 of Andrei Lupas's COILS2 for detailed and reliable coiled-coil predictions. 
		 Author:	Alex Knight, aek4@york.ac.uk
		 Home:	http://www.york.ac.uk/depts/biol/units/coils/coilcoil.html
		 Archive: iubio/mac/macstripe*
		 MacT M
		 MacT is a set of programs for the Macintosh to construct and evaluate 
		 unrooted trees derived from amino acid sequences using a distance matrix method.
		 Author:	Angela Luettke & Rainer Fuchs
		 Archive: ebi/mac/mact_*, iubio/mac/mact.*
		 Map Manager	M, W
		 Map Manager is a program which helps analyze the results of genetic 
		 mapping experiments using intercrosses with codominant markers, backcrosses or 
		 recombinant inbred strains in experimental plants or animals.	It is a specialized 
		 database program which allows easy storage, retrieval, and display of information from 
		 such mapping experiments, and it also has tools for searching and for statistical 
		 analysis of the experimental results.	These tools assist the user in determining 
		 linkage among loci and in determining the order of loci.		
		 Author:	Kenneth F. Manly, kmanly@mcbio.med.buffalo.edu
		 Home:	http,ftp://mcbio.med.buffalo.edu/
		 Archive: iubio/mac/map-manager*, ebi/mac/mapmanager*
		 MapMaker M, W, O
		 MapMaker is a linkage analysis package designed to help construct 
		 primary linkage maps of markers segregating in experimental crosses. One version 
		 performs full multipoint linkage analysis for dominant, recessive, and co- dominant 
		 (e.g.	RFLP-like) markers.
		 Author:	Whitehead Inst. for Biomedi. Res., mapmaker@genome.wi.mit.edu
		 Home:	ftp://genome.wi.mit.edu/distribution/mapmaker3
		 Archive: iubio/mapmaker/
		 Materials & Methods	M
		 A Hypercard stack for the storage & retrieval of laboratory procedures. 
		 The stack comes pre-loaded with many commonly-used procedures used in molecular 
		 biology.
		 Author:	James W. Brown, jwbrown@mbio.ncsu.edu
		 Archive: iubio/mac/mandm*, ebi/mac/matmeth*
		 Matilda	W
		 Matilda is a specialized DNA database management system that helps 
		 scientists extract the high-level information that they need for recombinant DNA 
		 experiments from a large sequence and genetic information database. It incorporates 
		 functional data and restriction map data.	Sequence and functional data are extracted 
		 from sequence files and from additional information. As recombinant DNA clones are 
		 constructed, their descriptions are added to the database so that they can be used to 
		 describe clones constructed later.
		 Author:	Isralewitz, B. & Shalloway, D.
		 Archive: iubio/ibmpc/matilda*
		 MatInspector M, W, O
		 MatInd is a simple but powerful method to derive a	 matrix description 
		 of a consensus from a number of short sequences	on which the definition of an IUPAC 
		 code would be based.		 MatInspector is a program that uses a large library of 
		 predefined matrix descriptions of transcription factor binding sites to locate matches 
		 in nucleotide sequences of unlimited length. It assigns a quality rating to matches and 
		 thus allows a quality- based filtering and selection of matches.
		 Author:	K.Quandt, et al, quandt@gsf.de
		 Home:	ftp://ariane.gsf.de/pub/
		 Archive: ebi/mac/matind*, ebi/dos/matind*
		 Memsat W, O
		 MEMbrane protein Structure And Topology.
		 Author:	David T. Jones, jones@bsm.bioc.ucl.ac.uk
		 Home:	ftp://ftp.biochem.ucl.ac.uk/pub/MEMSAT
		 Metree W
		 A package for inferring and testing minimum evolution trees. This 
		 package is intended to find the minimum 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 a publishable form.	 
		 Author:	Andrey Rzhetsky and Masatoshi Nei, aur1@psuvm.psu.edu
		 Archive: iubio/ibmpc/metree*
		 MitoProt M, O
		 It supplies a series of parameters that permit theoretical evaluation on 
		 mitochondrial targeting	sequences and the importability.	MitoProt II provides the 
		 possibility to predict mitochondrial proteins harboring targeting sequences.	 
		 Chloroplast proteins also can be studied.
		 Author:	Manuel G. Claros, claros@uma.es,	Pierre Vincens 
		 Home:	ftp://ftp.ens.fr/pub/molbio/, 
							ftp://ftp.rediris.es/software/incoming/science/
		 Archive: iubio/mac/mitprot*, ebi/mac/ 
		 Molwt	W
		 This program calculates molecular weight from an entered chemical 
		 formula, and gives concentrations in various units in response to an entered formula 
		 and concentration.		
		 Author:	John A. Kiernan, jkiernan@julian.uwo.ca
		 Archive: iubio/ibmpc/molwt*, ebi/dos/molwt*
		 Mufold (Mac) M
		 A MacOS port of Michael Zucker's MFold software for prediction of RNA 
		 secondary structure by free energy minimization,	 including sub optimal folding with 
		 temperature dependence. See also PCFold.
		 Author:	D. Gilbert (mac port), M. Zuker (MFold)
		 Home:	iubio/mac/mulfold*, ftp://snark.wustl.edu/pub/ (MFold)
		 Archive: ebi/mac/
		 NIH Image	M
		 Image can be used to measure the area, average density, center of 
		 gravity, and angle of orientation of a user defined region of interest.	It also 
		 performs automated particle analysis and can be used to measure path lengths and 
		 angles. 
		 Author:	Wayne Rasband
		 Home:	ftp://zippy.nimh.nih.gov/pub/nih-image/, 
							http://rsb.info.nih.gov/nih-image/
		 NJbafd W, O
		 These programs are for constructing a neighbor-joining or UPGMA tree 
		 from allele frequencies of microsatellite DNA or other genetic markers, and computing 
		 heterozygosities and Gst.
		 Author:	Naoko Takezaki, ntakezak@lab.nig.ac.jp
		 Archive: iubio/evolve/njbafd/
		 NJPlot M, W, O
		 NJPlot is a phylogenetic tree drawing program that handles	 files 
		 describing trees by the nested parentheses method (e.g. PHYLIP-built trees). Features: 
		 A graphical interface allows to re-root a tree anywhere and to swap branches. Bootstrap 
		 values are displayed next to internal branches. Branch lengths can be optionally 
		 displayed. Tree plots can be saved to a PostScript or PICT file.
		 Author:	Manolo Gouy, mgouy@biomserv.univ-lyon1.fr
		 Home:	ftp://biom3.univ-lyon1.fr/pub/mol_phylogeny/njplot
		 archive: ebi/mac/
		 Noncode	W
		 A program that will read an ESEE file containing nucleic acid sequences 
		 and produce a distance matrix using the Kimura 2-parameter model.
		 Author:	Eric L. Cabot, cabot@gcg.com
		 Archive: iubio/ibmpc/noncode*
		 Numclone W
		 Estimates the number of clones one has to screen from a genomic library 
		 in order to find a desired clone.
		 Author:	John Nash, Nash@biologysx.lan.nrc.ca
		 Archive: iubio/ibmpc/numclone*
		 Oligobase	W
		 This is a shareware program for Windows designed to organize and catalog 
		 oligonucleotides collection of a biological laboratory. It stores information about 
		 oligonucleotides, select subsets according to specified criteria, print out order 
		 forms, calculate molecular weight and melting temperature, and manipulate 
		 oligonucleotides.
		 Author:	Igor Sidorenkov, sidorenk@rocketmail.com
		 Home:	http://lochfort.com/oligobase
		 Archive: iubio/ibmpc/obase*
		 OligoCR	M
		 OligoCR is a data management tool for organizing and cataloging 
		 oligonucleotide collection. It allows you to store information about the oligos, e.g., 
		 the category (PCR, sequencing), type of project the oligo is used for, its application, 
		 its description. To search your oligo database, just click the mouse. It has the 
		 capability to proofread your sequences.
		 Author:	Yongming Sun, ysun@hdklab.wustl.edu
		 Home:	http://hdklab.wustl.edu/~ysun
		 Archive: iubio/mac/oligocr*
		 OligoMutantMaker W
		 OligoMutantMaker simplifies the designing and screening of 
		 oligonucleotide-directed single amino acid substitution experiments by searching for 
		 nucleotide sequences which introduce a restriction endonuclease recognition sequence 
						 into the codon substitution site of the mutant.
						 Author:	Kevin Beadles et al.
						 Archive: iubio/ibmpc/oligo*, ebi/dos/oligo*
						 Onix W
						 A 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 is interactive software with a high-performance 
						 interface, fast 3D molecular graphics and analysis of water-accessible surface.	
						 Author:	A.S.Ivanov et al., ivanov@ibmh.msk.su
						 Home:	ftp://org.chem.msu.su/pub/software/Onix/
						 P1 Clones	M
						 This is a simple HyperCard stack for keeping track of clones that were 
						 constructed with the bacteriophage P1 cloning system. 
						 Author:	Ken Abremski, sabremske@esvax.dnet.dupont.com
						 Archive: iubio/mac/p1clones*
						 PAML M, W, O
						 Phylogentic Analysis by Maximum Likelihood contains three main programs 
						 for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid 
						 sequence data.
						 Author:	Ziheng Yang, z.yang@ucl.ac.uk
						 Home:	ftp://abacus.gene.ucl.ac.uk/pub/paml
						 Archive: iubio/evolve/paml*
						 PcFold W
						 A PC version of Michael Zuker's RNA-folding program which uses an energy 
						 minimization algorithm to predict stem and loop regions of RNA structures. See also 
						 MulFold, and home site for Unix versions.
						 Author:	Michael Zuker et al., zuker@snark.wustl.edu
						 Home:	ftp://snark.wustl.edu/pub/
						 Archive: iubio/ibmpc/pcfold*, ebi/dos/pcfold
						 PHYLIP M, W, O
						 A PHYLogeny Inference Package of many programs for phylogenetic 
						 analysis, including parsimony, compatibility, distance matrix invariants ("evolutionary 
						 parsimony") and likelihood methods on various kinds of data.
						 Author:	Joseph Felsenstein, joe@genetics.washington.edu
						 Home:	http, ftp://evolution.genetics.washington.edu/
						 Archive: iubio/evolve/phylip*, ftp://ftp.nig.ac.jp/pub/unix/phylip, 
											ftp://ftp.bioss.sari.ac.uk/pub/phylogeny/phylip
						 Phylodendron M, W, O (Java)
						 Phylodendron is an application for drawing phylogenetic trees	It reads 
						 data in New Hampshire (Newick) format.	 Options allow you to adorn and edit the tree.		
						 Author:	D. Gilbert
						 Home:	iubio/java/apps/trees/
						 Phyltest W
						 A program for testing phylogenetic hypothesis, with comparison of three 
						 alternative phylogenetic trees, estimation of average pairwise distances, and others.
						 Author:	Sudhir Kumar, imeg@psuvm.psu.edu
						 Archive: iubio/ibmpc/phyltest*
						 Plasmid Processor	W
						 Plasmid Processor is a simple tool for plasmid presentation for 
						 scientific and educational purposes. It features both circular and linear DNA, user 
						 defined restriction sites, genes and multiple cloning site. In addition you	can 
						 manipulate plasmid by inserting and deleting fragments. Created drawings	 can be copied 
						 to clipboard or saved to disk for later use. Printing from	 within program is also 
						 supported. 
						 Author:	T. Kivirauma, P. Oikari and J.Saarela, Dept. of Biochemistry & 
											Biotechnology, U. of Kuopio, plasmid@uku.fi
						 Home:	http://www.uku.fi/~kiviraum/plasmid/plasmid.html
						 Archive: iubio/ibmpc/plasmid-processor*, ebi/dos/plasmid
						 Plasmid-Maker	M
						 Draws linear and circular plasmid	maps, allows borders of various 
						 widths and fills of grays, arrows, and other options.
						 Home:	http://yeamob.pci.chemie.uni-tuebingen.de/Archiv/PlasmidMaker.html
						 Archive: iubio/mac/plasmid-maker*
						 Author:	Kai-Uwe Froehlich, kaifr@uni-tuebingen.de
						 Primer Design	W
						 PrimerDesign is a DOS program to choose primer for PCR or 
						 oligonucleotide probes. It is tailored to check known	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. 
						 Additional features: unique sequences, repeats, restriction sites.
						 Author:	Andreas Becker, Joerg Napiwotzki, 
											becker@ps1515.chemie.uni-marburg.de
						 Home:	ftp://ftp.chemie.uni-marburg.de/pub/PrimerDesign
						 Primer		M, W, O
						 Primer is a computer program for automatically selecting PCR primers.	
						 It tests oligos for annealing temperature, complementarity to genomic repeat sequences, 
						 ability to form primer-dimer, and other criteria.	Primer annealing temperature 
						 calculation is based on thermodynamic parameters.	
						 Author:	Steve Lincoln et al., primer@genome.wi.edu
						 Home:	ftp://genome.wi.mit.edu/pub/software/Primer2.2
						 Archive:		iubio/primer/primer-wi*
						 Primer-Master	W
						 Automatically 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;
						 Author:	Proutski Vitali, Sokur Oleg, proutski@influenza.spb.su
						 Archive: ebi/dos
						 Primers!		M
						 Primers! is a primer design shareware application, written by the author 
						 of Whitehead Institute Primer2.	It allows users to interactively scroll through lists 
						 of forward and reverse primers to pick exactly the primer pair wanted.	 
						 Author:	Richard Resnick, rjr@applepi.com
						 Home:	http://www.applepi.com/
						 Archive:		iubio/mac/primers*
						 ProAnal	W
						 ProAnal	is for analysis of multiple protein alignments, studying the 
						 structure-function and structure-activity relationships in protein/peptide families.	 
						 The program uses aligned amino acid sequences with data of their activity and searches 
						 for correlations between data on activity and various physico-chemical characteristics 
						 of different regions in primary structures. 
						 Author:	Alexey Eroshkin, eroshkin@vector.nsk.su
						 Archive: iubio/ibmpc/proanal*, ebi/dos/
						 ProAnalyst W
						 ProAnalyst is for investigation of structural differences between 
						 proteins divided by functional, evolutionary or other criteria; structure-activity 
						 relationships investigation; searching motifs; protein-engineering experiments; and 
						 many other protein analysis functions.
						 Author:	Vladimir Ivanisenko, Alexey Eroshkin, eroshkin@vector.nsk.su
						 Archive: iubio/ibmpc/panalyst*, ebi/dos/proanalyst
						 ProAnWin W
						 Multiple sequence alignment, analysis of protein sequences and 
						 structures, structure-activity relationships, design of protein-engineering 
						 experiments. Threads multiple alignment onto known 3-dimensional structure; searches 
						 linear, spatial sites, conservative and variable in changes of specified 
						 physico-chemical properties; plots of different physico-chemical profiles for 
						 individual or a set of protein sequences; and many other functions.
						 Author:	I.Pika et al.,	eroshkin@vector.nsk.su
						 Archive: iubio/ibmpc/paw*, ebi/dos/proanwin
						 ProfileGraph W
						 A graphical protein analysis tool.
						 Author:	Kay Oliver Hofmann, khofmann@biomed.biolan.uni-koeln.de
						 Archive: iubio/ibmpc/prograph*, ebi/dos/pgraph*
						 PromFind W
						 PromFind is a DOS program that accepts a DNA sequence, and adds a 
						 feature table to annotate the location of putative promoter regions. 
						 Author:	Gordon B. Hutchinson, hutch@netshop.bc.ca
						 Archive: iubio/ibmpc/promfind*
						 ProMSED	W
						 ProMSED, 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 visual analysis are facilitated by group and 
						 block operations and amino acid coloring reflecting their similarity.
						 Author:	Anatoly Frolov, Alexey Eroshkin, eroshkin@vector.nsk.su
						 Archive: iubio/ibmpc/promsed*, ebi/dos/promsed/
						 Prophet	W, O
						 Prophet offers advanced, easy-to-use software tools for data management 
						 and visualization, and statistical analysis - from simple descriptive statistics to 
						 multi-factor ANOVA, logistic regression, and non-linear modeling.	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. 
						 Author:	Prophet software group, BBN, prophet-info@bbn.com
						 Home:	http://www-prophet.bbn.com/
						 Protein Sequence Analysis	W
						 The 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, secondary structure prediction, and 
						 others.
						 Archive: iubio/ibmpc/prot-sa*
						 Puzzle M, W, O
						 Puzzle is a maximum likelihood analysis for nucleotide, amino acid, and 
						 two-state data.	It reconstructs phylogenetic trees from molecular sequence data, and 
						 has a fast tree search that allows analysis of large data sets.	Puzzle is PHYLIP 
						 compatible.
						 Author:	Korbinian Strimmer, Arndt von Haeseler, 
											strimmer@zi.biologie.uni-muenchen.de
						 Home:	ftp://fx.zi.biologie.uni-muenchen.de/pub/puzzle
						 Archive: iubio/evolve/puzzle/, ebi/mac/puzzle, dos/puzzle, unix/puzzle
						 RAMHA	W
						 Monte Carlo simulation of the random mutagenesis of synthetic cDNAs.
						 Author:	David P. Siderovski, Siderovski@Galen.OCI.UToronto.CA
						 Archive: iubio/ibmpc/ramha*
						 RasMol M, W, O
						 RasMol is a molecular modelling program for the visualization of 
						 proteins and nucleic acids. It reads protein databank (PDB) files and interactively 
						 renders them in a variety of formats, including wire, stick, stick_and_ball, CPK, and 
						 ribbon.
						 Author:	R. Sayle, ros@dcs.ed.ac.uk
						 Home:	ftp://ftp.dcs.ed.ac.uk/pub/rasmol/
						 Archive: ftp://kekule.osc.edu/pub/chemistry/software/X-WINDOWS/rasmol*, 
											ebi/mac/rasmol*, software/dos/raswin*, 
						 Rbinding W
						 Calculates the number of binding sites and the affinities of cell 
						 surface receptors for ligands (Scatchard analysis).
						 Author:	Nico van Belzen & Joop van Zoelen, belzen@pa1.fgg.eur.nl
						 Archive: iubio/ibmpc/rbindin*
						 ReadSeq	M, W, O
						 A program for converting among several biosequence file formats.
						 Author:	Don Gilbert, software@bio.indiana.edu
						 Home:	iubio/readseq/
						 Archive: ebi/mac/readseq*
						 ReAlign	W
						 A program that realigns a DNA alignment according to a peptide 
						 alignment, thereby improving the alignment in areas not too well conserved.
						 Author:	Rasmus Wernersson, RWer@novo.dk
						 Archive: iubio/ibmpc/realign*
						 RepFind	W
						 RepFind (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.
						 Author:	Gordon B. Hutchinson, hutch@netshop.bc.ca
						 Archive: iubio/ibmpc/repfind*, ebi/dos/repfind*
						 Restdata W
						 Restriction data and phylogenetic analysis, computes the numbers of 
						 nucleotide substitutions per site for pairs of DNA sequences; constructs phylogenetic 
						 trees by using the neighbor-joining method.
						 Author:	Tatsuya Ota, imeg@psuvm.psu.edu
						 Archive: iubio/ibmpc/restdata*
						 RestSite W
						 Several programs for analyzing restriction site or fragment data for use 
						 in molecular systematics studies.
						 Author:	Joyce C. Miller
						 Archive: iubio/ibmpc/restsite*
						 RNA Dotplot	M
						 RNA Dotplot is a simple utility to print a dot matrix of the potential 
						 base pairing interactions in an RNA sequence. 
						 Author:	David S. McPheeters, mcpheeters@biochemistry.cwru.edu
						 Archive: iubio/mac/rna-dotplot*
						 Rnadraw	W
						 Rnadraw offers RNA optimal structure / basepair-probability matrix / 
						 heat curve calculation on Intel computers, providing a consistent user interface with 
						 many possibilities to view, print, import/export and edit calculation results.
						 Author:	Ole Matzura, ole@mango.mef.ki.se
						 Home:	ftp://broccoli.mfn.ki.se/pub/rnadraw
						 RNA_d2 W
						 RNA_d2 is a user-friendly program developed for interactively generating 
						 aesthetic and non-overlapping drawings of RNA	secondary structures. It allows easy 
						 untangling and editing of RNA molecules > 1000 nucleotides long.
						 Author:	J. Perochon-Dorisse et al., rnad2@ibcg.biotoul.fr
						 Home:	ftp://hpsrv.biotoul.fr/rna
						 Sagittarius Dna	W
						 A package for exon/intron structure revealing on the base of protein 
						 k-tuples statistic.
						 Author:	Victor B. Strelets, strelets@bio.indiana.edu
						 Archive: iubio/ibmpc/sag-exo*, ebi/dos/sag-exo
						 Sagittarius Pir	W
						 A highly compact databank variant of original PIR database designed to 
						 assist individuals in utilization of sequence database information without huge storage 
						 space requests.	 Includes fast homology searches and selection of sequences by fields 
						 (name, source, keyword, etc.), or (non)perfect homology with user-defined short 
						 sequence.
						 Author:	Victor B. Strelets, strelets@bio.indiana.edu
						 Archive: iubio/ibmpc/sag-pir*
						 Sagittarius Seqanalref W
						 A dialog shell for storage and manipulation of reference information. 
						 This particular variant is oriented on SEQANALREF databases compiled by A.Bairoch.
						 Author:	Victor B. Strelets, strelets@bio.indiana.edu
						 Archive: iubio/ibmpc/seqanalr*, ebi/dos/sag-sar*
						 Send W
						 A program for computing the standard errors of nucleotide diversity and 
						 divergence using the algorithm of Nei and Jin.
						 Author:	Li Jin
						 Archive: iubio/ibmpc/send*
						 Sendbs W, O
						 A program that computes average nucleotide substitutions within and 
						 between populations using the algorithm of Nei and Jin. It computes standard errors 
						 with a bootstrap method that differs from Nei and Jin's.
						 Author:	Naoko Takezaki, ntakezak@lab.nig.ac.jp
						 Archive: iubio/evolve/sendbs*
						 Seq-Eudora-Blast M
						 Macintosh AppleScript applications that automate your BLAST searches. 
						 Drag-and-dropped sequence files to the BLAST server at ncbi.nlm.nih.gov using Eudora 
						 mail. 
						 Author:	Brian Osborne, bosborne@nature.berkeley.edu
						 Home:	http://pgebaker4.pw.usda.gov/bio/bio.html
						 Archive::	iubio/mac/seq-eudora-blast*
						 Seqaid II	W
						 Seqaid 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 by codon bias. 
						 Author:	Donald Roufa & D.D. Rhoads
						 Archive: iubio/ibmpc/sequaid*, ebi/dos/sqaid*
						 SeqApp M
						 A Macintosh biosequence editor, analyzer, and network	handyman.	 See 
						 SeqPup.
						 Author:	D. Gilbert, seqapp@bio.indiana.edu
						 Home:	iubio/seqapp/
						 SeqPup M, W, O (Java) 
						 The successor to SeqApp, SeqPup is a biological sequence editor and 
						 analysis program.	It includes links to network 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 boxed and shaded regions, Internet searches, use of 
						 external analysis programs, including	ClustalW multiple alignment, CAP contig 
						 assembly, tacg restriction map,	and a remote client-server interface.	 The current 
						 version runs on any os supporting Java, an	 older version runs on MacOS, MSWin and some 
						 Unix.
						 Author:	D. Gilbert, seqpup@bio.indiana.edu
						 Home:	iubio/seqpup/
						 SeqSimPresenter	M
						 SeqSimPresenter converts a set of aligned sequences to shaded bars of 
						 which correspond to the degree of similarity.	It presents large alignments in a 
						 compact form and allows a fast recognition of the amount, extension, and distribution 
						 of conserved regions. 
						 Author:	cbkfr01@mailserv.zdv.uni-tuebingen.de
						 Archive: iubio/mac/seqsimpresent*, ebi/mac/
						 Sequin M, W, O
						 Sequin 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 short mRNA sequence, and complex 
						 submissions containing long sequences, multiple	annotations, segmented sets of DNA, or 
						 phylogenetic and	 population studies.
						 Author:	Jonathan Kans, Colombe Chappey, info@ncbi.nlm.nih.gov
						 Home:	ftp://ncbi.nlm.nih.gov/sequin/, http://www.ncbi.nlm.nih.gov/Sequin
						 SeqVu	M
						 An alignment editor with analysis options that allows you to work 
						 quickly and simply with multiple sequences. It is ideal for manually correcting 
						 alignments produced using software such as ClustalV.
						 Author:	James Gardner, j.gardner@garvan.unsw.edu.au
						 Home:	ftp://gimr.garvan.unsw.edu.au/pub/
						 Archive: iubio/mac/seqvu*
						 Shm	W, O
						 Shm was designed to provide assistance in the analysis of somatic 
						 (point) mutations induced in the immunoglobulin genes of B-lymphocytes. It builds 
						 clonal trees by	parsimony and displays them along with somatic mutations.
						 Author:	Laurentiu COCEA, cocea@necker.fr
						 Archive: iubio/ibmpc/shm*
						 Sigma	M, O
						 System for Integrated Genome Map Assembly graphical genome map editor.	 
						 As a viewer, Sigma puts full color maps of the genome in the users hands to display, 
						 browse, manipulate, and print. It is capable of giving 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 a 
						 variety of sources. A convenient user interface makes data entry easy.
						 Author:	Theoretical Biology and Biophysics Group at LANL, sigma@ncgr.org
						 Home:	http://www.ncgr.org/sigma/home.html
						 Archive: ebi/linkage_and_mapping/SIGMA
						 Silmut W
						 Silmut helps you to identify regions in a sequence which can be altered 
						 to introduce restriction enzyme sites and other sequences by silent mutations.
						 Author:	Raj Shankarappa,	bsh@med.pitt.edu, K. Vijayananda, 
											vijay@litsun.epfl.ch
						 Archive: iubio/ibmpc/silmut*
						 Sim2 M, W, O
						 This program build local alignments of two sequences, each of which may 
						 be hundreds of kilobases long.
						 Author:	Chao K-M et al., zjing@sunset.nlm.nih.gov
						 Home:	ftp://ncbi.nlm.nih.gov/pub/sim2
						 Sites	M, W, O
						 Sites is a program for the analysis of comparative DNA sequences. It is 
						 primarily intended for data with multiple closely related sequences.	 
						 Author:	 Jody Hey
						 Archive: iubio/evolve/sites/
						 SixcutterFreq	M
						 The 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. The algorithm is based on the frequency of 
						 dinucleotide pairs.
						 Author:	Brian Osborne, bosborne@nature.berkeley.edu
						 Archive: iubio/mac/sixcutterfreq*
						 Sneath ST	W
						 Statistical programs to screen a matrix of molecular sequences for 
						 atypical sequence comparisons, and to simulate the addition of constant sites to 
						 randomly-placed differences in a molecular sequence comparison.
						 Author:	P.H.A. Sneath, mjs@le.ac.uk
						 Archive: iubio/ibmpc/sneathst*
						 Solupred M, W
						 This spreadsheet allows one to predict the solubility of recombinant 
						 proteins in E. coli based on the amino acid content.
						 Author:	Roger Harrison & Dan Diaz, BL275@cleveland.freenet.edu
						 Archive: iubio/mac/solupred-mac*, ibmpc/solupred*
						 SorFind	W
						 SorFind is a DOS program that adds to DNA sequence files a feature table 
						 to annotate the location of putative coding exons.	 
						 Author:	Gordon B. Hutchinson, hutch@netshop.bc.ca
						 Archive: iubio/ibmpc/sorfind*, ebi/dos/sorfin*
						 Spectrum M, W
						 Spectrum is a Macintosh and MS Windows program to read in phylogenetic 
						 data in Nexus format, and display the bipartition spectra	corresponding to the data.	 
						 It can also be used to find the tree whose expected spectrum is closest to the observed 
						 spectrum. It outputs spectra in Microsoft Excel and other formats.
						 Author:	Michael Charleston, Roderic Page, m.a.charleston@bio.gla.ac.uk
						 Home:	http://taxonomy.zoology.gla.ac.uk/mike/spectrum/
						 Spombe-Strain	M
						 S.pombe strain collection is a Hypercard stack for cataloguing	 the 
						 genotypes of S.pombe yeast strains. It is adapted from Kai-Uwe Frölich's yeast strain.
						 Author:	Doug Drummond ddrummon@fs2.scg.man.ac.uk
						 Archive: iubio/mac/spombe-strain*
						 ssu rRNA M
						 This Hypercard stack contains the entire Ribosomal Database Project 
						 sequence release 1.	The sequences are accessible via a series of linked phylogenetic 
						 trees, a list, or by name.
						 Author:	James W. Brown, jwbrown@mbio.ncsu.edu
						 Archive: iubio/mac/ssu-rrna*
						 Swiss-PdbViewer	M, W
						 Swiss-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, for comparison of active 
						 sites. It can also measure distances, angles, torsions angles between atoms as well as 
						 add/remove amino acids from the view.	It includes many other features.
						 Author:	Nicolas Guex, Manuel Peitsch, ng45767@ggr.co.uk
						 Home:	ftp://expasy.hcuge.ch/pub/PDBViewers/Prot3Dviewer, 
											http://www.expasy.ch/spdbv/mainpage.html, 
											http://www.pdb.bnl.gov/expasy/spdbv/mainpage.htm
						 tacg M, W, O
						 A program for restriction enzyme and other analyses of DNA.	This is a 
						 command-line program that can be used from MacOS, Wintel through others such as SeqPup.
						 Author:	Harry Mangalam, mangalam@uci.edu
						 Home:	http://hornet.bio.uci.edu/~hjm/projects/tacg/
						 Archive: iubio/restrict-enz/tacg*
						 TFPGA	W
						 TFPGA (Tools for population genetic analyses) is a Windows program for 
						 the analysis of allozyme and molecular population genetic data.	The program calculates 
						 simple descriptive statistics, genetic distances, and F-statistics.	It also performs 
						 tests for Hardy-Weinberg equilibrium, population differentiation and performs UPGMA 
						 clustering and Mantel Tests.
						 Author:	Mark P Miller, mpm2@nauvax.ucc.nau.edu
						 Home:	http://dana.ucc.nau.edu/~mpm2
						 TopPredII	M
						 Prediction of transmembrane segments in integral membrane proteins, and 
						 the putative topologies.
						 Author:	Claros M.G & von Heijne G., claros@cica.es, gvh@cbs.ki.se
						 Archive: ebi/mac/, iubio/mac/toppred*
						 TOPS W, O
						 Program to automatically generate and edit protein	 topology cartoons. 
						 These cartoons are two dimensional representations of the secondary structure of 
						 proteins. 
						 Author:	Tom Flores, flores@ebi.ac.uk
						 Home:	ebi/pub/contrib/TOPS
						 Tree Draw Deck M
						 A Hypercard stack which draws phylogenetic trees. It is derived from 
						 Drawgram and Drawtree of Phylip by J. Felsenstein
						 Author:	D. Gilbert, software@bio.indiana.edu
						 Home:	iubio/mac/treedraw*
						 Archive: ebi/mac/treedraw*
						 Treecon	W
						 A package for the construction of phylogenetic trees. Its advantages 
						 include menu-driven, easy-to-use interface, quick, handles large datasets, large set of 
						 distance-measure methods and distance-matrix based tree construction tools, 
						 sophisticated options like subset resampling and test of outgroup influence, additional 
						 tools like production of partial alignments and indication of informative positions.
						 Author:	Yves Van de Peer, yvdp@reks.uia.ac.be
						 Home:	ftp://uiam3.uia.ac.be/
						 Archive: iubio/ibmpc/treecon*
						 TreeView M, W
						 A program for drawing phylogenies on MacOS and MS Windows. The program 
						 reads NEXUS, PHYLIP, Clustal W and similar tree formats. 
						 Author:	Roderic D M Page, r.page@bio.gla.ac.uk
						 Home:	http://taxonomy.zoology.gla.ac.uk/rod/treeview.html
						 Archive: iubio/mac/treeview*, iubio/ibmpc/treeview*
						 Vised	W
						 A 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 for many sequence file formats; 
						 supports extraction of sequences from library files; figure preparation; boxed output 
						 of sequence identities; imports MACAW alignments; protein sequence prediction in one or 
						 all six frames.
						 Author:	Ken Peters, kpeters@qb.island.net
						 Archive: iubio/ibmpc/vised*
						 Visual BLAST and FastA W
						 These programs are designed for interactive analysis of full BLAST and 
						 FASTA	output files containing protein sequence alignments.	They implement analytical 
						 tools which automate detailed analysis of BLAST and FASTA	outputs, and include tools 
						 for multiple alignment analysis.
						 Author:	Patrick Durand et al., durand@lmcp.jussieu.fr
						 Home:	http://www.lmcp.jussieu.fr/~durand/
						 WinDot W
						 A dotplot program for MS Windows.
						 Author:	Ramin Nakisa, ramin@ic.ac.uk
						 Archive: iubio/ibmpc/windot, ebi/dos/windot
						 WinMGM W
						 Visualisation and manipulation tools for proteins, nucleic acids and 
						 organic molecules, including manipulation of molecules represented as CPK, stick and 
						 ball, ribbons and cylinders, and colorations by atomic type, atoms of a selected area, 
						 of an active site, and others. Several other features are included.
						 Author:	Mehdi Rahman, Robert Brasseur, mehdirah@fsagx.ac.be
						 Home:	
											http://www.fsagx.ac.be/info_faculte/info_dep/info_bp/mehdi/winmgm/winmgmen.htm
						 WinSeq W, O
						 The ReadSeq program for converting among biosequence file formats, for 
						 MS Windows.
						 Author:	Ramin Nakisa, ramin@ic.ac.uk
						 Archive: iubio/ibmpc/winseq, ebi/dos/winseq, see iubio/readseq/ for 
											others
						 WPDB W
						 WPDB (the Protein Data Bank through MS Windows) is a package with a 
						 compressed version of PDB and a set of tools to query features of a single structure or 
						 perform a comparative analysis on multiple structures with emphasis on sequence 
						 alignment and structure superposition.
						 Author:	Ilya N. Shindyalov, Philip E. Bourne, bourne@sdsc.edu
						 Home:	ftp://ftp.sdsc.edu/pub/sdsc/biology/WPDB/
						 Yeast Strain M
						 This is a Hypercard stack for cataloguing 
						 the genotypes of S. cerevisiae yeast strains.
						 Author:	Kai-Uwe Froehlich, cbkfr01@mailserv.zdv.uni-tuebingen.de
						 Archive: iubio/mac/yeaststrain*, ebi/mac/
			
				 Index
						 Bio Catalog of software 2
						 Citing software 8
						 client-server 5
						 Clustal 5
						 CORBA 7
						 EMBOSS 5
						 Entrez 6
						 European Bioinformatics Institute (EBI) 2
						 File Transfer Protocol (FTP) 3
						 free software 1
						 genome data 6
						 Hypertext Transport Protocol (HTTP) 3
						 image analysis 6
						 IUBio Archive 2
						 Java 4
						 Macintosh 1
						 Microsoft 1
						 molecular modelling 7
						 Multi-platform software 4
						 National Center for Biotechnology Information (NCBI) 6
						 NIH Image 6
						 PHYLIP 6
						 phylogeny analyses 6
						 public domain 7
						 RasMol 7
						 Search Launcher 3
						 SeqPup 7
						 sequence alignment 5
						 sequence editing 7
						 software
								align
									 Clustal W 11
									 ClustalX 12
									 Lalnview 18
									 MACAW 19
									 ReAlign 28
									 SeqSimPresenter 30
									 SeqVu 30
									 Sim2 31
								chemistry
									 BufferStack 11
									 Cabuffer 11
									 Enzyme Kinetics 15
									 Gepasi 17
									 Hyper 18
									 Lines&Kinetics 18
									 Molwt 22
									 Rbinding 27
								codon
									 Codon Frequency Analyzer 12
									 CodonBiasIndex 12
									 GCUA 16
								databank
									 Automatic-BLAST 10
									 BCM Search Launcher 10
									 Entrez 15
									 FastA 15
									 MacPattern 19
									 Sagittarius Pir 29
									 Seq-Eudora-Blast 29
									 Sequin 30
									 Visual BLAST and FastA 34
									 WPDB 34
								dna
									 Annhyb 10
									 CAP 11
									 CGR 11
									 Comap 12
									 ConsInspector 12
									 Digest 13
									 Digispeak 13
									 DNA Runs 13
									 DNA Slider 13
									 DNA Stacks 13
									 Dna Workbench 14
									 DNAdraw 14
									 Double Digester 15
									 EditView 15
									 Gel 16
									 Gel Frag Sizer 16
									 HDProbe 17
									 HelixVu 18
									 Intron Analyzer 18
									 Matilda 21
									 MatInspector 21
									 Noncode 23
									 PromFind 26
									 RepFind 28
									 Sagittarius Dna 29
									 Silmut 31
									 SixcutterFreq 31
									 SorFind 32
									 tacg 33
								map
									 MacPlasmap 20
									 Plasmid Processor 24
									 Plasmid-Maker 25
									 Sigma 31
								molecular model
									 FoldIt 16
									 Onix 23
									 RasMol 27
									 Swiss-PdbViewer 32
									 WinMGM 34
								other
									 ADE-4 9
									 Gel Manager 17
									 Materials & Methods 21
									 NIH Image 22
									 Numclone 23
									 P1 Clones 23
									 RAMHA 27
									 Sagittarius Seqanalref 29
									 Shm 30
									 Sneath ST 31
									 Spombe-Strain 32
									 Yeast Strain 35
								pcr
									 Amplify 9
									 CPrimer 12
									 dPrimer 15
									 HyperPCR 18
									 Oligobase 23
									 OligoCR 23
									 OligoMutantMaker 23
									 Primer 25
									 Primer Design 25
									 Primer-Master 25
									 Primers! 25
								phylogeny
									 Ancestor 10
									 CAIC 11
									 Covariation 12
									 Dispan 13
									 fastDNAml 16
									 GeneTree 17
									 Lintr 19
									 MacT 20
									 Metree 21
									 NJbafd 22
									 NJPlot 22
									 PAML 24
									 PHYLIP 24
									 Phylodendron 24
									 Phyltest 24
									 Puzzle 27
									 Restdata 28
									 RestSite 28
									 Send 29
									 Sendbs 29
									 Sites 31
									 Spectrum 32
									 Tree Draw Deck 33
									 Treecon 33
									 TreeView 33
								population
									 DnaSP 14
									 Linkage-1 18
									 Map Manager 20
									 MapMaker 20
									 TFPGA 33
								protein
									 ABaCUS 9
									 AnalyzeSignalase 10
									 Antheprot 10
									 MacProt 20
									 MacStripe 20
									 Memsat 21
									 MitoProt 21
									 ProAnal 26
									 ProAnalyst 26
									 ProAnWin 26
									 ProfileGraph 26
									 Protein Sequence Analysis 27
									 Solupred 32
									 TopPredII 33
									 TOPS 33
								rna
									 LoopDLoop 19
									 Mufold (Mac) 22
									 PcFold 24
									 RNA Dotplot 28
									 Rnadraw 28
									 RNA_d2 28
									 ssu rRNA 32
								sequence
									 DCSE 12
									 DNAfrag 14
									 Dotplot 14
									 Dotty Plotter 15
									 Esee 15
									 GeneDoc 17
									 GeneMaster 17
									 MacBoxshade 19
									 ProMSED 26
									 Prophet 27
									 ReadSeq 28
									 Seqaid II 29
									 SeqApp 30
									 SeqPup 30
									 Vised 34
									 WinDot 34
									 WinSeq 34
						 Software listings 9
						 Wintel 1
.
