Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00023 NAME CLUSTAL V DOMAIN Alignment Search software DOMAIN Phylogeny DESCRIPTION Multiple sequence alignment AUTHOR Higgins D., Fuchs R. and Bleasby A.J. RA Higgins D.G., Bleasby A.J., Fuchs R.; RT "CLUSTAL V: improved software for multiple sequence alignment."; RL Comput. Appl. Biosci. 8:189-191(1992). RX Medline; 92274219. RX SeqAnalRef; HIGD9202. ADDRESS European Bioinformatics Institute ADDRESS Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK CONTACT Des.Higgins@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/align SITE-CONTACT gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison dbd@theory.bchs.uh.edu OS Unix, Vax/VMS LANGUAGE C VOLUME - COMMENTS This software may be distributed and used COMMENTS freely, provided that you do not modify it COMMENTS without the permission of the authors. AC BC00024 NAME CLUSTAL W DOMAIN Alignment Search software DOMAIN Phylogeny DESCRIPTION Multiple sequence alignment. It is a complete overhaul and DESCRIPTION upgrade of CLUSTAL V DESCRIPTION From version 1.4, it is ported to MAC and PC : DESCRIPTION Thave a nice beefy machine. On a Power Mac or a Pentium box DESCRIPTION it is nice and fast. Two precompiled versions are supplied for Macs DESCRIPTION (Power mac and old mac versions). DESCRIPTION Mac: 1500 residues by 100 sequences DESCRIPTION Power Mac 3000 " " " " DESCRIPTION PC 1500 " " " " AUTHOR Higgins D., Thompson J., Gibson T. RA Thompson J.D., Higgins D.G., Gibson T.J.; RT "CLUSTAL W: improving the sensitivity of progressive RT multiple sequence alignment through sequence weighting, RT position-specific gap penalties and weight matrix choice."; RL Nucleic Acids Res. 22:4673-4680(1994). RX Medline; 95075648. RX SeqAnalRef; THOD9402. ADDRESS European Molecular Biology Laboratory ADDRESS Meyerhofstrasse 1, 69117 Heidelberg, Germany CONTACT Gibson@embl-heidelberg.de ADDRESS EMBL Outstation, Hinxton - The European Bioinformatics Institute ADDRESS Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK CONTACT Des.Higgins@ebi.ac.uk SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix/clustalw.tar.Z UNIX software are SITE stored as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax/clustalw.uue VAX software are SITE stored as uuencoded (.UUE) files. SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/mac/clustalw.sea.hqx (self extracting archive/binhex) SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos/clustal$.exe (self extracting ZIP archive) SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/align SITE-CONTACT gilbertd@cricket.bio.indiana.edu SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE-CONTACT Dan Davison dbd@theory.bchs.uh.edu OS Vax/VMS, UNIX, MacOS, MS-DOS LANGUAGE C VOLUME - COMMENTS This software may be distributed and used COMMENTS freely, provided that you do not modify it COMMENTS without the permission of the authors. AC BC00074 NAME TREEALIGN DOMAIN Alignment Search software DOMAIN Phylogeny DESCRIPTION Multiple sequence alignment and phylogeny AUTHOR Hein J. RA Hein J.; RT "Unified approach to alignment and phylogenies."; RL Meth. Enzymol. 183:626-645(1990). RX Medline; 90190398. RX SeqAnalRef; HEIJ9001. ADDRESS - CONTACT - SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/unix UNIX software are stored SITE as archive (tar) files compressed (.Z). SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/vax VAX software are stored as SITE uuencoded (.UUE) files. SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/unix SITE ftp anonymous ftp.bchs.uh.edu (129.7.2.43)/ SITE Directory /pub/gene-server/vms SITE-CONTACT Dan Davison: dbd@theory.bchs.uh.edu OS Unix, Vax/VMS LANGUAGE C VOLUME - AC BC00166 NAME fastDNAml DOMAIN Phylogeny DESCRIPTION fastDNAml is a program derived from Joseph Felsenstein's version DESCRIPTION 3.3 DNAML(part of his PHYLIP package). DESCRIPTION fastDNAml is an attempt to solve the same problem as DNAML, DESCRIPTION but to do so faster and using less memory, so that larger trees DESCRIPTION and/or more bootstrap replicates become tractable. DESCRIPTION Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML DESCRIPTION program from PASCAL to C. AUTHOR G J. Olsen, H. Matsuda, R. Hagstrom, R. Overbeek RT - ADDRESS - CONTACT - SITE gopher Host: megasun.BCH.UMontreal.CA Port: 70 SITE URL gopher://megasun.BCH.UMontreal.CA:70/11/CMB/Phylogeny/fastDNAml SITE-CONTACT - OS UNIX LANGUAGE C VOLUME - AC BC00167 NAME MARKOV DOMAIN Phylogeny DESCRIPTION The program MARKOV computes a distance measure between pairs of DESCRIPTION nucleotide sequences. It also constructs phylogenies from these DESCRIPTION and summarizes the 4x4 substitution matrices between the pairs DESCRIPTION of species. It uses a more general model of substitution DESCRIPTION than used in PHYLIP, the Stationary Markov Model. AUTHOR G. Pesole, C. Lanave and C.Saccone RA Saccone C., Lanave C., Pesole G., Peparata G.; RT "Influence of base composition on quantitative estimates of gene RT evolution."; RL Meth. Enzymol. 183:570-583(1990). RX Medline; 90190394. RX SeqAnalRef; SACC9001. ADDRESS Dipartimento di Biochimica e Biologia Molecolare, ADDRESS Universita` di Bari, via Orabona 4, 70126 Bari, Italy. CONTACT cecilia@area.ba.cnr.it, graziano@area.ba.cnr.it SITE ftp anonymous area.ba.cnr.it SITE Directory /pub/programs/markov SITE-CONTACT - OS Vax/VMS, Unix (Sun OS) LANGUAGE FORTRAN, C VOLUME - AC BC00168 NAME MOLPHY DOMAIN Phylogeny DESCRIPTION MOLPHY is a program package for MOLecular PHYlogenetics. DESCRIPTION PROTML is a main program in MOLPHY for inferring evolutionary trees from DESCRIPTION PROTein (amino acid) sequences by using the Maximum Likelihood method. DESCRIPTION Programs (C language) DESCRIPTION - PROTML: Maximum Likelihood Inference of Protein Phylogeny DESCRIPTION - NUCML: Maximum Likelihood Inference of Nucleic Acid Phylogeny DESCRIPTION - PROTST: Basic Statistics of Protein Sequences DESCRIPTION - NUCST: Basic Statistics of Nucleic Acid Sequences DESCRIPTION - NJDIST: Neighbor Joining Phylogeny from Distance Matrix DESCRIPTION Utilities (Perl) DESCRIPTION -mollist: get identifiers list molrev: reverse DNA sequences DESCRIPTION -molcat: concatenate sequences molcut: get partial sequences DESCRIPTION -molmerge:merge sequences nuc2ptn: DNA -> Amino acid DESCRIPTION -rminsdel:remove INS/DEL sites molcodon: get 3rd(1st,2nd) codons DESCRIPTION -molinfo:get(non)information sites mol2mol: MOLPHY format beautifer DESCRIPTION -inl2mol: Interleaved -> MOLPHY mol2inl: MOLPHY -> Interleaved DESCRIPTION -mol2phy: MOLPHY -> Sequential phy2mol: Sequential -> MOLPHY DESCRIPTION -must2mol:MUST -> MOLPHY AUTHOR Jun Adachi, Masami Hasegawa RT - ADDRESS Jun Adachi, Department of Statistical Science, ADDRESS The Graduate University for Advanced Study ADDRESS 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106, Japan ADDRESS Masami Hasegawa,The Institute of Statistical Mathematics ADDRESS 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106, Japan CONTACT Jun Adachi adachi@ism.ac.jp CONTACT Masami Hasegawa hasegawa@ism.ac.jp SITE ftp anonymous sunmh.ism.ac.jp SITE Directory /pub/molphy SITE-CONTACT - OS Unix (SunOS 4.1.3 & HP-UX9.03) LANGUAGE C, Perl VOLUME - REQUIRES - AC BC00169 NAME PARBOOT DOMAIN Phylogeny DESCRIPTION PARBOOT is a parallel implementation of the bootstrapping DESCRIPTION function available in many of the PHYLIP phylogenetic analysis programs. DESCRIPTION The PARBOOT application splits a multiple-dataset inputfile into its DESCRIPTION independent datasets, and processes these datasets in parallel on multiple DESCRIPTION hosts (or one host with multiple CPUs). This means that the speed of a DESCRIPTION bootstrap analysis can be approximately improved in proportion the number DESCRIPTION and power of CPUs available to the user. AUTHOR Rioux P., Littlejohn T. RT - ADDRESS Departement de biochimie, Universite de Montreal ADDRESS CP 6128, Centre-ville, Montreal (Quebec), H3C 3J7, Canada CONTACT ogmp@bch.umontreal.ca SITE ftp anonymous megasun.bch.umontreal.ca SITE Directory /pub/parboot SITE-CONTACT Tim Littlejohn tim@bch.umontreal.ca SITE gopher Host: megasun.BCH.UMontreal.CA Port: 70 SITE URL gopher://megasun.BCH.UMontreal.CA:70/11/CMB/Phylogeny/ SITE-CONTACT Tim Littlejohn tim@bch.umontreal.ca OS Unix : SunOS and SGI LANGUAGE Perl VOLUME 25kb REQUIRES Networked Unix systems, An account on all hosts that will be used REQUIRES Working "rsh" and "rcp" commands REQUIRES The PHYLIP package accessible on all hosts AC BC00170 NAME PAUP DOMAIN Phylogeny DESCRIPTION A parsimony program. It allows multistate characters, DESCRIPTION user-defined weights on individual state DESCRIPTION transitions,Wagner, Camin-Sokal and Dollo DESCRIPTION parsimony methods, bootstrap confidence DESCRIPTION intervals, and finding all most parsimo- DESCRIPTION nious trees by branch-and-bound. It also has DESCRIPTION provision for computing Lake's linear DESCRIPTION phylogenetic invariants. AUTHOR - RT - ADDRESS - CONTACT - SITE - SITE-CONTACT - OS - LANGUAGE - VOLUME - COMMENTS PAUP will soon be distributed by Sinauer Associates, of Sunderland, COMMENTS Massachusetts, in versions that will do distance matrix methods COMMENTS as well as parsimony. AC BC00171 NAME PHYLIP DOMAIN Phylogeny DESCRIPTION A general purpose package of programs for inferring phylogenies, DESCRIPTION including parsimony, compatibility, invariants, distance DESCRIPTION computations, distance matrix methods, and maximum likelihood DESCRIPTION methods, as well as programs for plotting and rearranging DESCRIPTION trees. PHYLIP is the most widely distributed phylogeny DESCRIPTION package, with over 6,000 registered users, and it competes DESCRIPTION with PAUP to be the one responsible for the largest number of DESCRIPTION published phylogenies. It is available in source code and DESCRIPTION also as executables for DOS, Windows, and Macintosh and DESCRIPTION PowerMac. AUTHOR Joe Felsenstein, Akiko Fuseki, Andrew Keeffe, Sean Lamont, AUTHOR Hisashi Horino RA Felsenstein, J.; RT "PHYLIP -- Phylogeny Inference Package (Version 3.2)."; RL Cladistics 5: 164-166 (1989). ADDRESS Department of Genetics ADDRESS University of Washington ADDRESS Box 357360 ADDRESS Seattle, WA 98195-7360 ADDRESS USA CONTACT joe@genetics.washington.edu SITE WWW Server at URL http://evolution.genetics.washington.edu/phylip.html SITE ftp anonymous evolution.genetics.washington.edu SITE Directory /pub/phylip SITE-CONTACT joe@genetics.washington.edu SITE ftp anonymous bioss.sari.ac.uk SITE Directory /pub/phylogeny SITE-CONTACT frank@bioss.sari.ac.uk OS Unix,DOS,Windows3.1,Windows95,WindowsNT,MacOS LANGUAGE Ansi C VOLUME - REQUIRES works on most computers COMMENT Other ftp distribution sites for PHYLIP are usually not COMMENTS up to date. A list of machines that have server versions of COMMENTS PHYLIP available, which will analyze for you using PHYLIP, COMMENTS is available at the PHYLIP web site, as well as a list of COMMENTS Phylogeny Programs that is even more complete than the COMMENTS BioCatalog's list. AC BC00172 NAME STATALIGN DOMAIN Phylogeny DOMAIN Alignment Search software DESCRIPTION All widely-used methods of alignment and phylogeny inference DESCRIPTION make certain assumptions about sequence evolution. These DESCRIPTION assumptions may be implicit (e.g. the parsimony method for DESCRIPTION phylogeny reconstruction, the conventional dynamic programming DESCRIPTION algorithm for alignment inference) or they may be explicit. The DESCRIPTION methods implemented here are derived from evolutionary models DESCRIPTION with explicit assumptions. DESCRIPTION This set of programs estimates (via an expectation-maximization DESCRIPTION algorithm) parameters relevant to the evolutionary relationship DESCRIPTION between a pair of DNA or protein sequences. It performs DESCRIPTION pairwise alignment and allows reliability of alignment positions DESCRIPTION to be examined visually. Also, the phylogeny reconstruction DESCRIPTION method described in Thorne and Kishino (1992, MBE 9:1148-1162) DESCRIPTION is implemented. DESCRIPTION To understand these programs a bit better and find a list of DESCRIPTION relevant references, read the file ``statprogs.doc''. It may DESCRIPTION also be worthwhile to read the files ``arcs2ps.doc'' and DESCRIPTION ``trees.doc''. The latter two files respectively explain the DESCRIPTION alignment visualization and phylogeny reconstruction software. DESCRIPTION Use these programs at your own risk !! They can require massive DESCRIPTION amounts of computer time (don't attempt to use them if you don't DESCRIPTION have a workstation or better) and they are user-rude. A little DESCRIPTION familiarity with Unix, a computer that can compile C code, and DESCRIPTION ability to edit files are essential. Despite these drawbacks, DESCRIPTION the methods implemented here can yield comparatively accurate DESCRIPTION estimates of evolutionary parameters and relatively high quality DESCRIPTION alignments. DESCRIPTION For the most part, these programs were written by Jeff Thorne DESCRIPTION with intellectual help from Hirohisa Kishino, Gary Churchill, DESCRIPTION and Joseph Felsenstein. Sean Lamont and Kerry Neef supplied DESCRIPTION helpful programming tips. Leigh Thorne provided constructive DESCRIPTION comments. Programs not written by Jeff Thorne are part of the DESCRIPTION phylogeny inference package (PHYLIP) distributed by Joseph DESCRIPTION Felsenstein. Those programs from PHYLIP are noted in the DESCRIPTION following section. AUTHOR Jeff Thorne (see description for full list) RA Thorne J.L, Kishino H.; RL MBE 9:1148-1162(1992). ADDRESS Jeffrey Thorne ADDRESS Program in Statistical Genetics, Statistics Department ADDRESS North Carolina State University ADDRESS Raleigh NC 27695-8203, USA ADDRESS Tel: 1-(919) 515-1946 ADDRESS FAX: 1-(919) 515-7591 CONTACT thorne@stat.ncsu.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/evolve SITE-CONTACT D Gilbert: gilbertd@cricket.bio.indiana.edu OS Unix LANGUAGE C VOLUME - REQUIRES - AC BC00173 NAME TREETOOL DOMAIN Phylogeny DESCRIPTION Treetool is an interactive tool for displaying, editing, DESCRIPTION and printing phylogenetic trees. The tree is displayed visually DESCRIPTION on screen, in various formats, and the user is able to modify DESCRIPTION the format, structure, and characteristics of the tree. DESCRIPTION Trees may be viewed, compared, formatted for printing, DESCRIPTION constructed from smaller trees, etc... DESCRIPTION Treetool works with Newick format tree files (Paup and Phylip DESCRIPTION compatible). It handles multifurcating trees, branch lengths DESCRIPTION (evolutionary distances), rooted/unrooted trees, and multiple DESCRIPTION trees per file. It can print to a PostScript printer, or output DESCRIPTION PICT graphics for Macintosh drawing programs (MacDraw). AUTHOR Mike Maciukenas RT - ADDRESS - CONTACT mooch@phylo.life.uiuc.edu SITE gopher Host: megasun.BCH.UMontreal.CA Port: 70 SITE URL gopher://megasun.BCH.UMontreal.CA:70/11/CMB/Phylogeny/TreeTool SITE-CONTACT tim@bch.umontreal.ca SITE ftp anonymous rdp.life.uiuc.edu SITE Directory /rdp/programs/TreeTool SITE-CONTACT - OS Sun Sparc machines (Sun 4's), LANGUAGE C VOLUME - REQUIRES Xview toolkit AC BC00363 NAME Random Cladistics DOMAIN Phylogeny DESCRIPTION With it you can bootstrap/jackknife/PTP/generate random tree DESCRIPTION histograms and calculate confidence values on cladistic DESCRIPTION coevolutionary questions. It is a package that includes the DESCRIPTION following programs : DESCRIPTION PTP.EXE, HEYJOE.EXE, TREES.EXE, LANYON.EXE, DANRAN.EXE, DESCRIPTION RND.EXE, CHKLAN.EXE AUTHOR Mark E. Siddall RT - ADDRESS Virginia Inst. Marine Sci., Gloucester Point, VA, 23062, USA CONTACT mes@vims.edu SITE ftp anonymous zoo.toronto.edu SITE Directory /pub/random.exe SITE-CONTACT - OS DOS (PC) LANGUAGE - VOLUME - REQUIRES - COMMENTS random.exe is a self extracting utility and COMMENTS will explode the version executables as well as a COMMENTS morphological data file, a sequence data file, other COMMENTS related data files, a on-line and MS-WRD for DOS quide to COMMENTS Random Cladistics as well as Hennig86 (help on it, not the COMMENTS executable). AC BC00416 NAME CAIC DOMAIN Phylogeny DOMAIN Comparative analysis DESCRIPTION CAIC - a comparative analysis package for the Apple DESCRIPTION Macintosh. This application implements a suite of DESCRIPTION 'phylogenetically correct' comparative methods for DESCRIPTION data sets including continuous variables. AUTHOR Andy Purvis, Andrew Rambaut RA Purvis A., Rambaut A.; (1995) RT "Comparative analysis by independent contrasts (CAIC): RT an Apple Macintosh application for analysing comparative RT data."; RL Comp. Appl. in Biosci. 11(3):247-251(1995). ADDRESS Department of Zoology, University of Oxford ADDRESS South Parks Road, Oxford OX1 4JD, U.K. CONTACT andy.purvis@zoo.ox.ac.uk SITE ftp anonymous evolve.zps.ox.ac.uk SITE Directory /FTP/packages/CAIC SITE-CONTACT andrew.rambaut@zoo.ox.ac.uk SITE WWW Server at URL http://evolve.zps.ox.ac.uk/CAIC/CAIC.html OS MacOS LANGUAGE - VOLUME - REQUIRES System 6.0, 500Kb RAM AC BC00421 NAME HICLAS DOMAIN Phylogeny DESCRIPTION We have developed a new data model which is suitable for DESCRIPTION supporting semantically interacting dynamic views of hierarchic DESCRIPTION biological classifications. On the basis of our new data model, DESCRIPTION we have developed a prototype database system called HICLAS DESCRIPTION (HIerarchical CLAssification System); its domain is plant DESCRIPTION taxonomy. HICLAS is available through the Internet and an DESCRIPTION X-window interface has been implemented to support queries to DESCRIPTION classification data. There is a service that provides an DESCRIPTION electronic forum for discussion on the Hierarchial Taxonomic DESCRIPTION Database Classification system developed at Michigan State DESCRIPTION University. This list is managed by a listserver. For more DESCRIPTION information on the listserver, please send a message to DESCRIPTION listserv@genesys.cps.msu.edu with a message body of HELP. The DESCRIPTION following documents (and possibly more) are available through DESCRIPTION the listserv HICLAS archive: DESCRIPTION FAQ Frequently Asked Questions (and answers) DESCRIPTION HOW-TO-GET How to get a copy of the HICLAS front end DESCRIPTION taxon-paper.ps Postscript version of the Taxon paper. AUTHOR Sungwon Jung, Stephen Perkins, Yang Zhong, AUTHOR Sakti Pramanik, John Beamanta RA Jung S., Perkins S., Zhong Y., Pramanik S., Beaman J.; RT "A New Data Model for Biological Classification."; RL Comp. Appl. Biosci. 11(3):237-246(1995). ADDRESS Department of Computer Science ADDRESS A714 Wells Hall, Michigan State University ADDRESS East Lansing, MI 48825, USA CONTACT pramanik@cps.msu.edu SITE ftp anonymous genesys.cps.msu.edu SITE Directory /pub/hiclas SITE-CONTACT parmanik@cps.msu.edu OS SunOs LANGUAGE C, English VOLUME - REQUIRES X-Window, a Sybase backend AC BC00432 NAME Puzzle DOMAIN Phylogeny DESCRIPTION Puzzle is an ANSI C program that implements the quartet puzzling DESCRIPTION method for reconstructing tree topologies from character state DESCRIPTION data (DNA, amino acids). Puzzle is PHYLIP compatible. AUTHOR Korbinian Strimmer, Arndt von Haeseler RA Strimmer K., von Haeseler A. RT "Quartet puzzling: A quartet maximum likelihood method RT for reconstructing tree topologies."; RL In prep. (1995). ADDRESS Korbinian Strimmer ADDRESS MIPS, Max-Planck-Institute for Biochemistry, ADDRESS Am Klopferspitz 18a, D-82152 Martinsried/München, Germany. ADDRESS Arndt von Haeseler ADDRESS Max Planck Institute for Evolutionary Anthropology, ADDRESS Inselstr. 22, D-04103 Leipzig, Germany. CONTACT arndt@haeseler@eva.mpg.de CONTACT strimmer@mips.biochem.mpg.de SITE WWW Server at URL http://members.tripod.de/korbi/puzzle/ SITE-CONTACT strimmer@mips.biochem.mpg.de SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/ SITE-CONTACT nethelp@ebi.ac.uk SITE ftp anonymous ftp.pasteur.fr SITE Directory /pub/GenSoft SITE-CONTACT letondal@pasteur.fr SITE ftp anonymous iubio.bio.indiana.edu SITE Directory /molbio/evolve SITE-CONTACT archive@bio.indiana.edu SITE ftp anonymous ftp.pasteur.fr SITE Directory /pub/GenSoft SITE-CONTACT letondal@pasteur.fr OS MacOS (PPC), Windows 95/98/NT,UNIX and VMS (src provided) LANGUAGE ANSI C VOLUME - COMMENTS The software is licensed under GPL REQUIRES ANSI C compiler COMMENTS Precompiled executables available for Mac 68k FPU and Mac PPC. COMMENTS Puzzle is also tested on UNIX (Makefile is available). COMMENTS Puzzle should run on all systems where an ANSI C compiler is COMMENTS available. COMMENTS Puzzle is PHYLIP compatible, it has the "look and feel" of a COMMENTS typical PHYLIP program, and it reads PHYLIP sequential COMMENTS formatted data. AC BC00444 NAME DERANGE2 DOMAIN Phylogeny DESCRIPTION The program sorts permutations issued from two gene DESCRIPTION sequences by using weigthed inversions, transpositions DESCRIPTION and inverted transpositions. AUTHOR Blanchette Mathieu, Sankoff David RT - ADDRESS Centre de Recherches Mathematiques ADDRESS Universite de Montreal ADDRESS Montreal, Quebec, Canada CONTACT blanchet@hans.crm.umontreal.ca SITE ftp anonymous ftp.ebi.ac.uk SITE-CONTACT Directory /pub/software/unix OS Unix, Sun, Dos LANGUAGE Standard C VOLUME Source:70K REQUIRES - AC BC00461 NAME DNA Stacks DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence editor DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genome Mapping Databases DOMAIN Phylogeny DESCRIPTION DNA Stacks (v. 1.1) is a HyperCard 2.x stack package DESCRIPTION for Macintosh computers featuring utilities for editing or DESCRIPTION coloring multiple DNA or protein sequence alignments, DESCRIPTION performing numerous data conversions or analyses related to DESCRIPTION molecular systematics, displaying auto-rescalable gene maps DESCRIPTION of mitochondrial or chloroplast genomes, extracting DNA DESCRIPTION gene sequences or translated protein sequences from about DESCRIPTION 26 animal mitochondrial genomes, and graphically depicting DESCRIPTION codon usage patterns. AUTHOR Eernisse, Douglas J. RA Eernisse, D. J.; RT "DNA Translator and Aligner: HyperCard utilities to aid RT phylogenetic analysis of molecules."; RL Comput. Appl. Biosci. 8:177-184(1992). RX Medline; 92274217. RX SeqAnalRef; EERD9201. ADDRESS D. J. Eernisse ADDRESS Dept. Biol. Sci. MH282 ADDRESS California State University ADDRESS Fullerton, CA 92634, USA CONTACT deernisse@fullerton.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/mac/ SITE-CONTACT archive@bio.indiana.edu SITE gopher Host: gopher://ftp.bio.indiana.edu Port: 70 SITE URL gopher://gopher://ftp.bio.indiana.edu:/70/11/IUBio-Software+Data/molbio/mac SITE WWW Server at URL http://biology.fullerton.edu/people/faculty/doug-eernisse/ OS MacOS LANGUAGE HyperTalk, C VOLUME 2 MB REQUIRES HyperCard 2.0 or greater, Macintosh AC BC00469 NAME OSA DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Epidemiology DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION OSA is a program to find, within an alignment of DESCRIPTION large sequences, those regions with an informative content DESCRIPTION similar to the displayed by the whole alignment and select, DESCRIPTION among them, the shortest empiricaly significant ones. The use of DESCRIPTION these short regions, instead of the larger ones, can save a DESCRIPTION considerable amount of time and resources in molecular screening DESCRIPTION or molecular epidemiology studies. AUTHOR Maria Jesus Martin, Joaquin Dopazo RA Martin M.J., Gonzalez-Candelas F., Sobrino F., Dopazo J.; RT "A method for determining the position and size of optimal RT sequence regions for phylogenetic analysis."; RL J. Mol. Evol. 41:1128-1138(1995). ADDRESS R&D Department, TDI ADDRESS c/ Condes de Torreanaz, 5 ADDRESS 28028, Madrid ADDRESS SPAIN CONTACT martin@tdi.es CONTACT dopazo@tdi.es SITE ftp anonymous ftp.tdi.es SITE Directory /pub/programas/ SITE-CONTACT martin@tdi.es SITE WWW Server at URL http://www.tdi.es/programas/osa-i.htm OS UNIX (Solaris, Irix) LANGUAGE GPC Pascal VOLUME 300K REQUIRES GPC for compiling sources COMMENTS OSA is available as both : executable file for Solaris or COMMENTS Irix operating systems and sources files. GPC compiler is COMMENTS only necessary if you download the sources. AC BC00479 NAME TreeView DOMAIN Phylogeny DESCRIPTION View and print phylogenetic trees on Apple Macintosh DESCRIPTION and Windows personal computers. Program reads NEXUS, DESCRIPTION PHYLIP, ClustalW and Hennig86 tree files. Supports native DESCRIPTION fonts and graphics formats (PICT and Windows metafiles), DESCRIPTION print preview and drag and drop opening of files. AUTHOR Roderic D. M. Page RT - ADDRESS Division of Environmental and Evolutionary Biology ADDRESS Institute of Biomedical and Life Sciences ADDRESS University of Glasgow ADDRESS Glasgow G12 8QQ, UK CONTACT r.page@bio.gla.ac.uk SITE WWW Server at URL http://taxonomy.zoology.gla.ac.uk/rod/treeview.html OS MacOS, Windows 3.x, Windows 95/NT LANGUAGE - VOLUME - REQUIRES - AC BC00488 NAME GeneDoc DOMAIN Alignment editing and display DOMAIN Protein sequence analysis DOMAIN Phylogeny DESCRIPTION GeneDoc is a full featured Multiple Sequence Alignment Editor DESCRIPTION and Shading Utility. GeneDoc is also intended to help you bring DESCRIPTION your genetics research work to publication with lots of shading, DESCRIPTION page and font layout features. This is a utility that reads either DESCRIPTION .MSF Multiple Sequence alignment files or can Import Fasta Format DESCRIPTION files to be saved as a .MSF file project. DESCRIPTION GeneDoc is an alignment editor, that is it allows you to Edit the DESCRIPTION Alignment so that different residues from each sequence are lined DESCRIPTION up with each other. This is accomplished by moving the residues in DESCRIPTION one (or all but one) sequence relative to the other sequences by DESCRIPTION inserting or deleting gaps. GeneDoc also features the exclusive DESCRIPTION Grab and Drag mode, arranging residues like beads on a string. A DESCRIPTION residue editing mode is available to allow you to change the DESCRIPTION residues values themselves. Built in DayHoff and BlockSum scoring DESCRIPTION functions allow you to be sure your alignment changes are DESCRIPTION improving the score. Scores can be determined either by a Sum of DESCRIPTION Pairs method or with the Phylogenetic tree support. GUI DESCRIPTION implimentation makes it all so easy to use! DESCRIPTION GeneDoc also provides a comprehensive range of Display Shading DESCRIPTION Modes, functions and capabilities. Outlined below, these functions DESCRIPTION give flexible ways to look at the data and to show important DESCRIPTION concepts. Shading can even be done manually! DESCRIPTION GeneDoc provides output many different ways. You can print DESCRIPTION directly to the printer, export BitMaps, Text or MAC style Pict DESCRIPTION files. AUTHOR Karl Nicholas, Hugh Nicholas, PhD. RT - ADDRESS Karl Nicholas ADDRESS 566 Vallejo St. #34 ADDRESS San Francisco, CA, 94133 CONTACT ketchup@cris.com SITE WWW Server at URL http://www.cris.com/~ketchup/genedoc.shtml OS Win/3.1,Win/95,Win/NT LANGUAGE - VOLUME - REQUIRES - AC BC00489 NAME DISTREE DOMAIN Phylogeny DESCRIPTION DISTREE computes pairwise distances (substitution rates) of DESCRIPTION aligned nucleotide sequences utilizing various models of base DESCRIPTION substitution. Moreover it provides the user with information DESCRIPTION on the goodness of fit of the models to the given set of DESCRIPTION sequence data. Each of the models is implemented in two DESCRIPTION variants, assuming identical and gamma distributed DESCRIPTION substitution rates across sequence sites. AUTHOR Johannes Schaefer, Michael Schoeniger RT - ADDRESS Lehrstuhl fuer Theoretische Chemie ADDRESS Technische Universitaet Muenchen ADDRESS Lichtenbergstr. 4 ADDRESS D-85747 Garching ADDRESS Phone: +49-89-289 13610 ADDRESS Fax: +49-89-289 13622 CONTACT schaefer@theochem.tu-muenchen.de CONTACT schoeniger@theochem.tu-muenchen.de SITE WWW Server at URL http://evol10.theochem.tu-muenchen.de/pub OS Unix, DOS LANGUAGE C VOLUME - REQUIRES - COMMENTS DISTREE is easy to install. This has been tested on different COMMENTS unix platforms. An ANSI C compiler is not required. COMMENTS DISTREE automatically detects inputs files written in COMMENTS GenBank, EMBL or PHYLIP interleaved format, and provides COMMENTS output files (trees and distance matrices) in a PHYLIP COMMENTS compatible format. AC BC00507 NAME NJPLOT DOMAIN Protein sequence analysis DOMAIN Sequence analysis DOMAIN Phylogeny DESCRIPTION NJPLOT is a phylogenetic tree drawing program that handles DESCRIPTION files describing trees by the nested parentheses method DESCRIPTION (e.g. PHYLIP-built trees). DESCRIPTION Features: DESCRIPTION A graphical interface allows to re-root a tree anywhere and DESCRIPTION to swap branches. DESCRIPTION Bootstrap values are displayed next to internal branches. DESCRIPTION Branch lengths can be optionally displayed. DESCRIPTION Tree plots can be saved to a PostScript file (a PICT file DESCRIPTION on Macintosh) for printing. AUTHOR Manolo Gouy RT - ADDRESS Laboratoire de biometrie, genetique et biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne, France CONTACT mgouy@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/mol_phylogeny/njplot SITE-CONTACT - OS DOS, Unix, Macintosh LANGUAGE - VOLUME - REQUIRES - AC BC00508 NAME PHYLO_WIN DOMAIN Phylogeny DESCRIPTION A graphical interface for numerous tree-making DESCRIPTION methods Phylo_win is a mouse-driven interface for molecular DESCRIPTION phylogenetic purposes. It displays a sequence alignment and DESCRIPTION allows an easy selection of sequences and sites to analyse. DESCRIPTION Trees are recovered according to most usual tree-making DESCRIPTION algorithms including maximum parsimony, maximum likelihood and DESCRIPTION numerous distance based methods. A bootstrap analysis may be DESCRIPTION performed with any of the above metohds. Trees may be drawn, DESCRIPTION printed, saved into files. Species group, site sets and trees DESCRIPTION may be saved into the data file for subsequent analyses. An DESCRIPTION on-line help makes phylo_win easy to use. AUTHOR Nicolas Galtier RT - ADDRESS Laboratoire de biometrie, genetique et biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne, France CONTACT galtier@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/mol_phylogeny/phylo_win SITE-CONTACT - OS Sun/Solaris, Sun/SunOs, DEC/Alpha, HP, OS SGIr5-IRIX, IBM-AIX, linux on 386/486/586 processors LANGUAGE ANSI C VOLUME - REQUIRES - AC BC00509 NAME SEAVIEW DOMAIN Alignment editing and display DOMAIN Phylogeny DESCRIPTION A multiple sequence alignment editor DESCRIPTION Features: DESCRIPTION A graphical interface allows to edit alignment gaps DESCRIPTION in one or several sequences simultaneously. DESCRIPTION Lists of sequences and of sites can be built. DESCRIPTION The dot-plot method can be applied and used as a guide for DESCRIPTION manual alignment. DESCRIPTION If the CLUSTALW program is installed, SEAVIEW can run it DESCRIPTION on selected sequences and sites to have them aligned. DESCRIPTION Reads and writes alignment files in formats: CLUSTAL, DESCRIPTION PHYLIP, GCG's MSF, FASTA and MASE. AUTHOR Manolo Gouy RT - ADDRESS Laboratoire de biometrie, genetique et biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne, France CONTACT mgouy@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/mol_phylogeny/seaview SITE-CONTACT - OS Sun/Solaris, Sun/SunOs, DEC/Alpha, HP, OS SGIr5-IRIX, IBM-AIX, linux on 386/486/586 processors LANGUAGE - VOLUME - REQUIRES - AC BC00528 NAME Bielefeld University Bioinformatics Server DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Alignment Search software DOMAIN Genetic tools DOMAIN Phylogeny DOMAIN WWW server SERVER http://bibiserv.TechFak.Uni-Bielefeld.DE/ DESCRIPTION BibiServ is both, a fast computer to run web-based DESCRIPTION bioinformatics software and an integration point for DESCRIPTION the bioinformatics activities at Bielefeld University. AUTHOR multiple authors RT - ADDRESS University of Bielefeld ADDRESS Technische Fakultaet, AG PI ADDRESS PB 100 131 ADDRESS D - 33501 Bielefeld ADDRESS Germany CONTACT bibi@TechFak.Uni-Bielefeld.DE SITE WWW Server at URL http://bibiserv.TechFak.Uni-Bielefeld.DE/ OS any LANGUAGE English VOLUME - REQUIRES Netscape Navigator > 3.0 AC BC00542 NAME Spectrum DOMAIN Sequence analysis DOMAIN Phylogeny DESCRIPTION SPECTRUM is a new Macintosh. and Microsoft. Windows. program DESCRIPTION designed to read in phylogenetic 4-state or binary data in DESCRIPTION NEXUS format, and display the bipartition spectra DESCRIPTION corresponding to the data. DESCRIPTION It can also be used to find the tree whose expected spectrum DESCRIPTION is closest to the observed spectrum (the "closest tree"). DESCRIPTION SPECTRUM outputs spectra in Microsoft. Excel format as DESCRIPTION tab-delimited text files and trees as TREEVIEW files. AUTHOR Michael A. Charleston, Roderic D. M. Page RT - ADDRESS Graham Kerr Building, ADDRESS D.E.E.B., ADDRESS I.B.L.S., ADDRESS University of Glasgow, ADDRESS Glasgow G12 8QQ, ADDRESS Scotland, U.K. CONTACT m.a.charleston@bio.gla.ac.uk SITE WWW Server at URL http://taxonomy.zoology.gla.ac.uk/mike/spectrum/spectrum.html OS MacOS, Microsoft. Windows '95/NT LANGUAGE C++ VOLUME approx. 600 kbytes REQUIRES 8 Mbytes RAM COMMENTS This is a beta-version: any comments, suggestions and COMMENTS problems should be sent to Mike Charleston at the e-mail COMMENTS address given. COMMENTS It is free but please register it so I can keep users up to COMMENTS date with new releases and bug fixes. AC BC00561 NAME ClustalX DOMAIN Alignment Search software DOMAIN Alignment browser DOMAIN Phylogeny DESCRIPTION ClustalX is a new windows interface for the ClustalW DESCRIPTION alignment program. The sequence alignment is displayed in a DESCRIPTION window on the screen, with pull-down menus providing all the options DESCRIPTION from ClustalW. DESCRIPTION DESCRIPTION New features: cut-and-paste operations; highlighting of DESCRIPTION conserved features; selection of a subset of sequences or a DESCRIPTION sub-range to be realigned; alignment quality analysis DESCRIPTION highlighting low-scoring regions. DESCRIPTION DESCRIPTION Available for SUN Solaris, SGI IRIX5, Digital UNIX for DEC, DESCRIPTION MS Windows (32 bit) for PC, Linux ELF for x86 PC, Macintosh DESCRIPTION PowerMac. AUTHOR Thompson J.D, Gibson T.J, Plewniak F, Jeanmougin F, Higgins D.G. RA Thompson J.D, Gibson T.J, Plewniak F, Jeanmougin F, Higgins D.G.; RA "The ClustalX windows interface: flexible strategies for RA multiple sequence alignment aided by quality analysis tools."; RL Nucleic Acids Res. 25:4876-4882(1997). ADDRESS IGBMC, ADDRESS Parc d'Innovation, ADDRESS Illkirch-Graffenstaden, ADDRESS France. CONTACT julie@igbmc.u-strasbg.fr SITE ftp anonymous ftp-igbmc.u-strasbg.fr SITE Directory pub/ClustalX SITE-CONTACT jeanmougin@igbmc.u-strasbg.fr OS UNIX,MS-Windows,Linux,MAC LANGUAGE C VOLUME - REQUIRES - COMMENTS Executables available for listed machines AC BC00562 NAME GeneTree DOMAIN Phylogeny DESCRIPTION GeneTree is a program for comparing gene and species DESCRIPTION trees using reconciled trees. The program can compute DESCRIPTION the cost of embedding a gene tree within a species tree, DESCRIPTION visually display the location and number of gene DESCRIPTION duplications and losses, and search for optimal species DESCRIPTION trees. AUTHOR Roderic D. M. Page RA Page, R. D. M., Charleston, M. A.; RT "From gene to organismal phylogeny: Reconciled trees and RT the gene tree/species tree problem." RL Molecular Phylogenetics and Evolution 7:231-240 (1997). ADDRESS Division of Environmental and Evolutionary Biology ADDRESS Institute of Biomedical and Life Sciences ADDRESS Graham Kerr Building ADDRESS University of Glasgow ADDRESS Glasgow G12 8QQ, UK CONTACT r.page@bio.gla.ac.uk SITE WWW Server at URL http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html OS Mac OS, Windows 95/NT 4.0 LANGUAGE - VOLUME - REQUIRES Either a PowerMac running Mac OS 7.5 or later, REQUIRES or an Intel-based PC running Windows 95/NT 4.0 or later COMMENTS A manual is available in Adobe Acrobat PDF format from the COMMENTS GeneTree Web site. Please email the author to obtain information COMMENTS about bug fixes and updates. AC BC00564 NAME SEALS: A System for Easy Analysis of Lots of Sequences DOMAIN Sequence format conversion tools DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Pattern Identification DOMAIN Genome Analysis DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DESCRIPTION SEALS (A System for Easy Analysis of Lots of Sequences) is a DESCRIPTION free, public domain package for large-scale sequence analysis DESCRIPTION investigations. It is still under development, but already DESCRIPTION provides a number of very useful programs, including unique DESCRIPTION taxonomy-aware tools. AUTHOR Walker DR, Koonin EV RA Walker DR, Koonin EV; RT "SEALS: A System for Easy Analysis of Lots of Sequences"; RL ISMB 5:333-339(1997). ADDRESS D Roland Walker ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS National Institutes of Health, Bldg. 38A ADDRESS Bethesda, MD 20894, USA ADDRESS Voice: +1 (301)435-5909 Fax: +1 (301)435-5909 ADDRESS email: walker@ncbi.nlm.nih.gov ADDRESS ADDRESS Eugene V. Koonin, PhD ADDRESS National Center for Biotechnology Information ADDRESS National Library of Medicine ADDRESS National Institutes of Health, Bldg. 38A ADDRESS Bethesda, MD 20894, USA ADDRESS Voice: +1(301)435-5913 Fax:+1 (301)480-9241 ADDRESS email: koonin@ncbi.nlm.nih.gov CONTACT walker@ncbi.nlm.nih.gov (Roland Walker) SITE WWW Server at URL http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html OS Unix LANGUAGE Perl VOLUME 150 MB REQUIRES a number of other programs and db detailed on the home page AC BC00570 NAME RASA 2.2 DOMAIN Sequence analysis DOMAIN Structure prediction DOMAIN Pattern Identification DOMAIN Phylogeny DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION RASA 2.2 provides a set of tools for measuring DESCRIPTION phylogenetic signal and for studying its distribution DESCRIPTION among taxa. DESCRIPTION DESCRIPTION This software is used for DESCRIPTION * measuring signal DESCRIPTION * testing the suitability of available outgroup taxa DESCRIPTION * detecting long branches in the taxon variance plot DESCRIPTION * performing the mixed-character taxon test for differential DESCRIPTION lineage sorting DESCRIPTION * performing bootstrap power and effect to examine the DESCRIPTION power curve for your data. DESCRIPTION DESCRIPTION Exploratory options include DESCRIPTION * determining the signal spectrum for a set of sequences DESCRIPTION * removing noisy sites DESCRIPTION DESCRIPTION Some researchers have used the software to examine DESCRIPTION hypotheses of alignment using phylogenetic signal as the DESCRIPTION criterion. DESCRIPTION DESCRIPTION This software can be used on discrete data (molecular, DESCRIPTION morphological, or mixed). AUTHOR James Lyons-Weiler, PhD RA Lyons-Weiler, J., Hoelzer, G.A. and Tausch R.J.; RT "Relative Apparent Synapomorphy Analysis (RASA) I: RT the statistical measurement of phylogenetic signal."; RL Molecular Biology and Evolution 13:749-757(1996). RA Lyons-Weiler, J. and Milinkovitch, M.C.; RT "A phylogenetic approach to the problem of differential RT lineage sorting."; RL Molecular Biology and Evolution 14:968-975(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RT "Escaping from the Felsenstein Zone by detecting long RT branches in phylogenetic data."; RL Molecular Phylogenetics and Evolution 8:375-384(1997). RA Lyons-Weiler, J. and Hoelzer, G.A.; RL "Optimal outgroup analysis."; RL Biological Journal of the Linnean Society 64:493(1998). RA Milinkovitch, M.C. and Lyons-Weiler, J.; RT "Finding optimal outgroup topologies and convexities RT when the choice of outgroups is not obvious."; RL Molecular Phylogenetics and Evolution 9:348-357(1998). ADDRESS - CONTACT jfl8@psu.edu SITE WWW Server at URL http://test1.bio.psu.edu/LW/list.htm OS Mac/PowerPC REQUIRES All superfluous extensions off. COMMENTS The software will be updated and bugs fixed at COMMENTS irregular intervals. Watch for updates. AC BC00579 NAME Pyramids DOMAIN Protein sequence analysis DOMAIN Genome Analysis DOMAIN Phylogeny DESCRIPTION PYRAMIDS is a set of programs to create and draw a DESCRIPTION pyramidale representation of a set of sequences (given DESCRIPTION their relative distance). DESCRIPTION a pyramidal representation is a planar graph (close DESCRIPTION to upgma-like trees). DESCRIPTION DESCRIPTION one of the key feature of a pyramidal representation, DESCRIPTION is that a sequence can belong to two cluster. AUTHOR Jean-Christophe Aude. RA Aude J.C. , Diaz-Lazcoz Y. , Codani J.J. and Risler J.L.; RT "Application of the pyramidal clustering method to RT biological objects"; RL Computer & Chemistry, special issue - [accepted] ADDRESS Universite Versailles/Saint-Quentin - CGM/CNRS, FRANCE CONTACT jean-christophe.aude@inria.fr SITE WWW Server at URL http://genome.genetique.uvsq.fr/Pyramids OS SunOS, Solaris, Linux, Digital Unix, SGI Irix LANGUAGE - VOLUME 150ko REQUIRES transfig for postscript conversion (optional) COMMENTS A java application that allow you to display the pyramid COMMENTS is also available from the web site. AC BC00588 NAME DAMBE (Data analysis in molecular biology and evolution) DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genetic tools DOMAIN Molecular Evolution DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DOMAIN General tools DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION DAMBE (Data Analysis in Molecular Biology DESCRIPTION and Evolution) is an integrated software package for DESCRIPTION converting, manipulating, statistically and graphically DESCRIPTION describing and analyzing molecular sequence data, with a DESCRIPTION user-friendly Windows 95 interface. AUTHOR Xuhua Xia RT - ADDRESS Department of Ecology & Biodiversity, ADDRESS University of Hong Kong, Hong Kong CONTACT xxia@hkusua.hku.hk SITE WWW Server at URL http://web.hku.hk/~xxia/software/software.htm OS Windows 95 LANGUAGE - VOLUME 10 MB REQUIRES Windows 95