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Mark Wilkinson, of the Department of Zoology, The Natural History Museum, London, U.K. (marw@nhm.ac.uk) has produced REDCON, a program to implement his method of reduced consensus trees. These find a tree with possibly fewer species that satisfies a strict or a majority rule consensus criterion. REDCON reads trees in PAUP* format. It is a DOS executable, and is available at his software Web site at http://www.bio.bris.ac.uk/research/markwilk/software.htm.

Mark Wilkinson, of the Department of Zoology, The Natural History Museum, London, U.K. (marw@nhm.ac.uk) has produced TAXEQ2, a program to carry out Safe Taxonomic Reduction, which means dropping some species to get a set whose phylogenetic relationships are less ambiguous. The method is described in Wilkinson's Ph.D. thesis (1992, Department of Geology, University of Bristol) and an example of its use will be found in the paper by Wilkinson, M. 1995. Coping with missing entries in phylogenetic inferences using parsimony. Systematic Biology 44: 435-439. TAXEQ2 is distributed as a DOS executable with documentation and sample data set from his software Web site at http://www.bio.bris.ac.uk/research/markwilk/software.htm.

Lars Jermiin and Olena Anpilogova ( jermiin@angis.usyd.edu.au), when Jermiin was at the Human Genetics Group, John Curtin School of Medical Research, Australian National University have produced TreeCons version 1.0. It generates a weighted consensus tree from trees obtained by maximum likelihood analysis, generates relative likelihood support on edges in this and other user-specified trees, and does the Kishino-Hasegawa test with any level of significance. It reads output files and tree files produced by some of the programs in PHYLIP, MOLPHY and TrExMl. The output file from TreeCons is in a format that then is fed back into PHYLIP's program Consense. A number of weighting schemes to compute tree weights from their likelihoods are allowed. The weighting schemes and the underlying theory are described in a paper: Jermiin L. S., G. J. Olsen, K. L. Mengersen, and S. Easteal. 1997. Majority-rule consensus of phylogenetic trees obtained by maximum likelihood analysis. Molecular Biology and Evolution 14: 1296-1302. TreeCons is distributed as C source code. It is available, with documentation and sample input and output, from its web site at http://jcsmr.anu.edu.au/dmm/humgen/lars/treeconssub.htm.

Joseph Thorley of the School of Biological Sciences, University of Bristol, U.K. (j.l.thorley@bris.ac.uk) and Rod Page of the University of Glasgow have written RadCon, a program to compute consensus trees. It is intended in future releases to also compute distances between trees. It can compute strict, Adams, and majority-rule consensus trees, and a number of others as well, including a consensus supertree method. It is currently available as a test version which expires at the start of the next month, so that a new version needs to be fetched once a month. This will change when the first full version is released. RadCon is a MacOS executable for MacOS 7.5 or later. RadCon is available at its web site at http://taxonomy.zoology.gla.ac.uk/~jthorley/radcon/radcon.html and its manual can also be downloaded or viewed from there.

George Estabrook of the Department of Biology, University of Michigan, Ann Arbor, Michigan (Estabrook@umich.edu) has written QUARTET2, which calculates measures of difference between phylogenies based on quartets (subtrees of four tips). The methods are described in a paper: Estabrook, G. F. 1992. Evaluating undirected positional congruence of individual taxa between two estimates of the phylogenetic tree for a group of taxa. Systematic Biology 41: 172-177. QUARTET2 is available as a DOS executable from his web page of computer programs at http://www-personal.umich.edu/~gfred/.

Ross Crozier (genrhc@lure.latrobe.edu.au) of the Department of Genetics and Human Variation, Latrobe University, Bundoora, Victoria, Australia and and Paul-Michael Agapow (p.agapow@ic.ac.uk) have written CONSERVE, version 3.1.2, a Macintosh program to use phylogenetic information to calculate biodiversity and test the feasability of conservation schemes. It measures the distinctiveness of species using genetic distances and also to test whether particular assemblages of populations preserve statistically significantly more biodiversity than other assemblages. Biodiversity is determined using GD (probability of more than one allele) or PD (length of evolutionary history) methods, from data in the form of unrooted trees produced in standard treefile format. It is available as a Macintosh executable in a self-extracting archive from its web site at http://evolve.bio.ic.ac.uk/software/conserve/index.html or an alternative web site at http://www.cs.latrobe.edu.au/~agapow/Software/.

George Weiller, of the Bioinformatics Group at the Research School of Biological Sciences of the Australian National University, Canberra (weiller@rsbs.anu.edu.au) has released TreeDis version 2.0. TreeDis finds the patristic distances (total length of branches between all pairs of taxa in a phylogeny. It takes as input the tree file in Newick standard form or in the format for NJTREE. It is distributed as a DOS executable (a C++ source code version can also be obtained from Weiller). It is available from its web site at http://life.anu.edu.au/molecular/software/tredis/.

Andrew Purvis of the Department of Biology, Imperial College, Silwood Park, U.K. (a.purvis@ic.ac.uk) and Andrew Rambaut (andrew.rambaut@zoo.ox.ac.uk) of the Department of Zoology, University of Oxford, England, have written CAIC (Comparative Analysis of Independent Contrasts), version 2.6. It is a Macintosh program that carries out the contrasts method (like my CONTRAST) but with some modifications by others to cope with lack of resolution of the phylogeny. It will run on any Macintosh, and is available free from CAIC's Web page http://evolve.bio.ic.ac.uk/software/caic/index.html or (in an earlier version) by anonymous ftp from directory packages/CAIC at evolve.zoo.ox.ac.uk. It is described in the paper by A. Purvis and A. Rambaut (1995) Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data. Computer Applications in the Biosciences (CABIOS) 11: 247-251.

Emília P. Martins (emartins@work.uoregon.edu), of the University of Oregon, has released version 4.0 of COMPARE, a package of programs for comparative methods analysis. COMPARE includes various programs for conducting statistical analyses of comparative data in a phylogenetic context. At the moment, it includes programs to compute independent contrasts, do spatial autocorrelation analyses, sum of squares parsimony, generate random data, trees and/or branch lengths, and various other things. New programs will be added as they are ready. COMPARE is written in Java and is available both as standalone Java (including source code) and also as a Compare server. It requires a Java runtime environment. COMPARE is available from its web site at http://work.uoregon.edu/~COMPARE/. Earlier Windows95 and Sun Solaris executables and C source code of COMPARE 3.1 are available from the COMPARE 3.1 web site at http://work.uoregon.edu/~COMPARE/indexV3.html and and Windows95, Windows3.1, Sun Solaris, and HP/UX executables as well as C source code of COMPARE 2.0 are available from the COMPARE 2.0 web site at http://work.uoregon.edu/~ftp/download.html.

Hang-Kwang Luh, John Gittleman, and Mark Kot of the University of Tennessee at Knoxville have made available PA, a package of Macintosh programs that implement the phylogenetic autocorrelation comparative method introduced by Gittleman and Kot ( Systematic Zoology , 1990). It is free and is available by anonymous ftp from ftp.math.utk.edu in directory pub/luh.

Emilia Martins (emartins@work.uoregon.edu), of the Department of Biology of the University of Oregon, has written CMAP, the Comparative Method Analysis Package, for comparative methods analysis. This package was developed when she and Ted Garland were conducting the simulation study described in the paper: Martins, E. P. and T. Garland, Jr. 1991. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45: 534-557. It can be used to estimate the correlation between two continuous characters measured in different species while taking phylogenetic information into account. Methods for doing so include several versions of Felsenstein's (1985) independent contrasts, and the sum-of-squared-changes parsimony algorithm. The programs in CMAP are described by Martins as "slow" and "unfriendly". The executables are available only for DOS machines. She is no longer developing this package, and is now concentrating her efforts on her other package COMPARE, which will soon be able to do everything that CMAP can. CMAP is available from its Web page at http://work.uoregon.edu/~emartins/programs/cmap.html or by anonymous ftp from evolution.uoregon.edu in directory CMAP.

Patrik Lindenfors (Patrik.Lindenfors@zoologi.su.se), of the Department of Zoology, Stockholm University, has written CoSta version 1.03, a DOS program which carries out the Contingent States Test for the correlation of changes in two characters along a tree, which is described in the paper: Sillén-Tullberg, B. 1993. The effect of biased inclusion of taxa on the correlation between discrete characters in phylogenetic trees. Evolution 47: 1182-1191. The program reads MacClade data files, and also text files saved from MacClade. The program can be fetched at its Web site at http://www.zoologi.su.se/personal/patrik/costa.html.

Ted Garland, of the Department of Zoology of the University of Wisconsin (tgarland@facstaff.wisc.edu) and his colleagues (Jason A. Jones, Allan W. Dickermann, Peter E. Midford, and Ramon Diaz-Uriarte) have developed PDAP version 5.0, Phenotypic Diversity Analysis Programs, a series of DOS programs to perform various comparative analyses. At present, the following phylogenetically based statistical methods are included: independent contrasts, squared-change parsimony reconstructions of ancestral states and estimation of evolutionary correlations, and phylogenetic analysis of covariance via computer-simulated (Monte Carlo) null distributions. PDTREE can also read, write, and edit trees. PDAP is described in a web page at http://www.wisc.edu/zoology/faculty/fac/Gar/PDAP.html. The methods used are described in a number of recent papers by these authors, including: Diaz-Uriarte, R., and T. Garland, Jr. 1996. Testing hypotheses of correlated evolution using phylogenetically independent contrasts: sensitivity to deviations from Brownian motion. Systematic Biology 45: 27-47, and Purvis, A., and T. Garland, Jr. 1993. Polytomies in comparative analyses of continuous characters. Systematic Biology 42: 569-575. PDAP is described PDAP is distributed by email of a self-extracting executable file, obtainable for free (contact Garland by e-mail). Alternatively, a DOS disk can be mailed.

David Ackerly (dackerly@leland.Stanford.EDU) of the Department of Biological Sciences, Stanford University, Stanford, California has released ACAP 2 (Another Comparative Analysis Program) to carry out independent contrasts methods for comparative analysis. It also also incorporates linear parsimony methods into the program, in order to calculate consistency indices for continuous characters. The program is written in Think Pascal for Macintosh systems, and is available from its web site at http://www.stanford.edu/~dackerly/ACAP.html as a Macintosh executable which will run on Macintosh or PowerMacintosh computers.

Simon Blomberg, of the Department of Zoology and Entomology of the University of Queensland, St. Lucia, Australia (S.Blomberg@mailbox.uq.edu.au) has announced the beta-release of a small comparative method program, Fels-Rand version 0.91beta [look folks, don't blame me, I had nothing to do with naming this program]. It is designed to analyse data when the phylogeny is only poorly known, as when there is one or several polytomies. The program is said to be inspired by a 1994 paper in Systematic Biology by Jonathan Losos. It retains known tree topology and randomises the unknown parts of the tree, unlike some other programs, which randomize the whole tree. The statistics are calculated on independent contrasts from fully (randomly) resolved trees. Fels-rand is written in XLISP-STAT, and runs in the XLISP-STAT environment (in other words you first must get and install XLISP-STAT on your computer to run the code, which is written in the XLISP-STAT language). XLISP-STAT is available for Macintosh, Windows, and Unix. Fels-rand is available from Blomberg's home page at http://dingo.cc.uq.edu.au/~ansblomb/. Its README file can be found in a newgroup posting at http://life.biology.mcmaster.ca/~brian/evoldir/Other/ComparativeMethod.software.

Ehab Abouheif (abouheif@duke.edu) of the Department of Zoology, Duke University, Durham, North Carolina has written (together with J. Reeve) Phylogenetic Independence version 1.1. It carries out Abouheif's Test For Serial Independence (TFSI) on continuously valued characters and his Runs Test on discretely valued characters. These are described in his paper: Abouheif, E. 1999. A method to test the assumption of phylogenetic independence in comparative data. Evolutionary Ecology Research 1: 895-909. The program is available as a Windows95/98/NT executable, and its manual may be viewed as a web pade, at its web site at http://life.bio.sunysb.edu/ee/ehab.

Dolph Schluter (schluter@zoology.ubc.ca) of the Department of Zoology of the University of British Columbia, in Vancouver, Canada, has released ANCML, a program which estimates ancestor states for a continuous trait, and provides a "standard error" for the marginal distribution of each estimate. The method is described in Schluter, D., T. Price, A. Ø. Mooers and D. Ludwig. 1998. Likelihood of ancestor states in adaptive radiation. Evolution 51: 1699-1711. The method assumes a Brownian motion model for the evolution of the trait. ANCML was written by modifying the program CONTRAST in PHYLIP version 3.5, and it uses similar input conventions. ANCML is available from its web page at http://www.zoology.ubc.ca/~schluter/ancml.html. It is available as generic C source code and as a SunOS executable or as a DOS executable.

Bill Bruno (billb@lanl.gov) of the Theoretical Biology and Biophysics Group T10, Los Alamos Scientific Laboratory, has produced RIND, (Reconstructed INDependence), a program which takes a tree supplied by the user, or uses a distance method of the users choosing (one which can be found in PHYLIP), and computes a maximum likelihood estimate of the number of times each residue in aligned protein sequences was replaced in each position. The method is described in: Bruno, W. J. 1996, Modeling residue usage in aligned protein sequences via maximum likelihood Molecular Biology and Evolution 13: 1368-1374. RIND is available as C source code for a Unix environment, and assumes that PHYLIP is also installed.

Joaquin Dopazo of the R&D Department of TDI (TDI-EMBNet), Spain, (dopazo@samba.cnb.uam.es) has written a program ABLE (Analysis of Branch Length Errors) which implements the method described by Adell and Dopazo in J. Mol. Evol. 38: 305-309 (1994). This is a parametric bootstrap test of constancy in evolutionary rates. The idea of the test is to simulate a large number of a data sets under the model of rate constancy and then to examine the distribution of the branch lengths. After, a tree is reconstructed without the constraint of rate constancy it can be checked whether the observed branch length values fall within the expected distribution. The program is intended for use with the PHYLIP programs FITCH and KITSCH. It is available as a DOS executable from Dopazo's software web page at http://www.cnb.uam.es/~bioinfo/Software/Ximo/www1.html or by anonymous ftp at: ftp.cnb.uam.es in directory pub/cnb/molevol.

Kent Fiala (72470.1407@compuserve.com) (most recently of SAS Institute) produced CLINCH (CLadistic INference by Compatibility of Hypothesized characters) version 6.2. It is a general-purpose compatibility program capable of handling multiple unordered states. It is available as a DOS executable, including FORTRAN source code, from the Digital Taxonomy web page at http://www.geocities.com/RainForest/Vines/8695/software.html#Cladistics.

Benjamin Salisbury (ben@aya.yale.edu), of the Department of Ecology and Evolutionary Biology, Yale University has released SECANT version 2.2, based on an earlier program, CLINCH, by Kent Fiala, now of SAS Institute. SECANT was previously known as CLINCH2. It is probably the most sophisticated compatibility analysis (clique analysis) program, capable of handling unordered multiple states. It can also group characters by Salisbury's own Strongest Evidence criterion. It and its criteria are described in a paper: Salisbury, B. A. 1999. Strongest evidence in compatibility: clique and tree evaluation using apparent phylogenetic signal. Taxon 48: 755-766. SECANT is available as a Windows95/NT executable, and its source code is described as available on request. It is available from its web page at http://jkim.eeb.yale.edu/salisbur/.

Mark Wilkinson, of the Department of Zoology, The Natural History Museum, London, U.K. (marw@nhm.ac.uk) has written PICA95, a package of programs for character weighting and randomization tests for compatibility analysis for 0/1 or multistate characters. These carry out a variety of tests for nonrandomly compatible characters and include methods developed by Sharkey, Le Quesne, Meacham and Alroy. They include ability of process data that reflect the splits method of Bandelt and Dress. The programs are available as a package of DOS executables, from his software Web site at http://www.bio.bris.ac.uk/research/markwilk/software.htm.

Christopher Meacham (Museum Informatics Project, University of California, Berkeley, California 94720, U.S.A.) produces COMPROB, a Pascal program to compute probabilities that characters would be compatible at random, thus telling us which clique is "most surprising". He can be contacted as meacham@violet.berkeley.edu about receiving a copy. The program is free.

The program MARKOV computes a distance measure between pairs of nucleotide sequences. It also constructs phylogenies from these and summarizes the 4x4 substitution matrices between the pairs of species. It uses a more general model of substitution than used in PHYLIP, the Stationary Markov Model described in the paper by Saccone et. al. in Methods in Enzymology volume 183, pages 570-583, 1990. Bootstrapping is used to analyze the statistical error of the results. Output files from CLUSTAL and PILEUP, as well as some other formats, can be used for input, and analysis can be confined to certain codon positions in coding sequences. The program is written in FORTRAN and runs on VMS and Unix systems. It was produced by Dr. Graziano Pesole and Professor Cecilia Saccone at the University of Bari, Italy, and is available (for free?) from Dr. Cecilia Lanave at CSMME-CNR, Dipartimento di Biochimica e Biologia Molecolare, Universita` di Bari, via Orabona 4, 70126 Bari, Italy. Her phone number is 39-80-243305, her fax number is 39-80-243317, and her e-mail address is lanave@vaxba0.ba.it or mvx36@ibacsata.it

J. S. Armstrong, A. J. Gibbs, R. Peakall and G. Weiller, (johna@rsbs-central.anu.edu.au) of Gibbs's group at the Research School of Biological Sciences of the Australian National University, Canberra, have produced RAPDistance version 1.04, a package for DOS or Windows systems for computing distance matrices for RAPD analyses. It has a comprehensive range of options for creating data files, editing them and using application programs to analyse them. RAPDistance is available free on the World Wide Web at http://life.anu.edu.au/molecular/software/rapd.html, or by anonymous ftp from directory pub/RAPDistance at life.anu.edu.au.

P. R. Reeves and colleagues at Sydney University, Australia, have produced MULTICOMP, a program for computing various distances from sequence data. It is described in a paper by Reeves et. al. in CABIOS 10: 281-284 (1994). I do not know what computer systems it runs on. Reeves may be contacted at reeves@angis.su.oz.au for distribution information.

Ken Rice (krice@saul.cis.upenn.edu) of the University of Pennsylvania (formerly of Harvard University) has produced RSVP (restriction site variability program) which calculates several measures of genetic variability based on restriction map data. It also produces Jukes-Cantor corrected distance matrices with standard errors from collections of restriction maps. C source code for Version 2.08 of RSVP is available free by anonymous ftp from: phylogeny.harvard.edu in directory pub/rice. It runs under Unix.

Microsat, by Eric Minch (minch@crick.stanford.edu) is a program for calculating distances from microsatellite data. It uses the methods developed by David Goldstein et. al., and presented in their papers of 1995 in Proc. Natl. Acad. Sci. USA 92: 6720-6727 and Genetics 139: 463-471. The distance is based on the mean microsatellite array size, implementing the "Delta mu" distance that they defined, which corrects for within-population variability and provides a distance that is independent of population size. It is available for free from a page in Luca Cavalli-Sforza's lab web site at http://human.stanford.edu/microsat/microsat.html. The program is written in ANSI C. Source code is distributed, and so are executables for DOS, PowerMac and Macintosh.

Georg Weiller, of the Bioinformatics Laboratory, Australian National University, Canberra, Australia (weiller@rsbs-central.anu.edu.au) has produced DIPLOMO (DIstance PLOt MOnitor) version 1.03. It compares different distance measures with each other by displaying them as a scatter plot. It then helps one instantly identify all individual comparisons within the plot. individual taxa can be excluded or included in the plots, DIPLOMO enables you to see whether different taxa have different mutational characteristics (such as more having relatively more transitions in some lineages), and whether different distance measures correlate. The program takes as input a file with several different distance matrices. This file is in a simple format which can readily be produced by editing distance matrices produced by other packages. A program to compute the distance matrices is currently under development. Although DIPLOMO is intended to be ported to multiple platforms the current version runs on DOS on PC-compatibles. DIPLOMO is free; it can be obtained by World Wide Web from http://life.anu.edu.au/molecular/software/diplomo/, or by anonymous ftp from life.anu.edu.au in /pub/molecular_biology/software/diplomo. Floppy disk distribution is also possible. It is described in a publication: Weiller, G. F. and A. Gibbs. 1995. DIPLOMO: The tool for a new type of evolutionary analysis. CABIOS 11: 535-40.

Joaquin Dopazo and J. M. Carazo ( jd19662@ggr.co.uk and carazo@embnet.cnb.uam.es) have produced SOTA, a package to carry out the Self Organizing Tree Algorithm. It is based on Kohonen's unsupervised neural network of self-organizing maps and on Fritzke's growthing cell structures algorithm to construct phylogenetic trees from biological molecular sequence data. It is described in a paper: Dopazo, J. and J. M. Carazo. 1997. Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree. Journal of Molecular Evolution 44a: 226-233. SOTA can use sequence data, distance matrix data, or dipeptide frequencies from proteins. SOTA is available as source code in C for Unix, as executables for SGI workstations, and also with a Windows program called Drawer that draws the resulting trees. The package with documentation is available by anonymous ftp from ftp.cnb.uam.es in directory pub/cnb/sota.

MUST, a package of sequence management programs, is distributed on a shareware basis by Herve Phillippe, of the Laboratoire de Biologie Cellulaire (URA CNRS 1134 D), Batiment 444, Universite de Paris-Sud, 91405 Orsay cedex, France. His e-mail address is hp@bio4.bc4.u-psud.fr, and his phone and fax numbers are respectively 33.1.69.41.64.81 and 33.1.69.41.21.30. MUST is available for free if you send 5 1.44-Mb diskettes, or on a shareware basis (with $100 registration fee) if you do not send diskettes. It runs on DOS systems using DOS version 3 or later. It is intended as complementary to existing phylogeny and alignment programs and can produce output files in the formats of PHYLIP, PAUP*, Hennig86, and CLUSTAL. It contains a variety of sequence input, editing, checking, and storage functions, as well as a sequence editor and a phylogeny plotter. It also allows further analyses of the results from these phylogeny programs. It is not yet available by ftp.

Steve Smith, formerly of the Harvard Genome Laboratory, has written an X-Windows interactive sequence editor, GDE (Genetic Data Environment), version 2.2, which allows the user to edit sequences and align them by hand, and to select subsets of sites and sequences and call a variety of analysis proprams including ClustalV and many of the PHYLIP 3.5 programs. The GDE 2.2 system will run on many workstations that have the X windowing system. It also includes the TreeTool tree-plotting program (see below). GDE 2.0 is free and is available for at the molecular biology software servers, a web page is at http://ftp.bio.indiana.edu/soft/molbio/unix/GDE/ and by anonymous ftp from megasun.bch.umontreal.ca in directory pub/gde. At the latter location there are also Linux binaries and Sun binaries.

Don Gilbert (gilbertd@bio.indiana.edu) of the Department of Biology of the University of Indiana, has written SeqPup version 0.7,, a biological sequence editor and analysis program usable on Macintosh, MS-Windows and X-Windows systems. It includes links to network services and external analysis programs. It includes phylogenetic analysis of alignments with the fastDNAml and LSADT programs. It can be obtained by anonymous ftp from iubio.bio.indiana.edu, in directory molbio/seqpup, or by World Wide Web at http://iubio.bio.indiana.edu/soft/molbio/seqpup. The most recent version of SeqPup is written in the Java language, and does not exist as an executable, since you can run the Java code directly if you have the Java 1.1 system (which is available on Windows, Macintoshes, and X Windows Unix systems). An earlier version (0.5) is available in C++, and executables of that are available for Macintosh (PowerMac and 68K), MS Windows (Win95, WinNT and Win3), and Unix/XWindows systems including Sun Solaris, SGI Irix, DEC Unix, Linux. It is currently the more complete version, since it can also run some PHYLIP programs. The C++ source code for that version available by anonymous ftp at: iubio.bio.indiana.edu in directory util/dclap/source/.

Wolfgang Ludwig and Oliver Strunk of the Lehrstuhl für Mikrobiologie of the Technische Universität München (wolfgang.ludwig@biol.chemie.tu-muenchen.de) distribute ARB, an environment for 16s/18s/23s ribosomal RNA sequence data. It provides a windowing environment for building up databases of RNA sequences, aligning them, and searching, editing, modifying, aligning, profiling, and constructing trees. ARB uses its own RNA sequence databases which are made available to ARB over the Web. For phylogenies it uses programs from PHYLIP and fastDNAml, as well as its own ARB Neighbor-Joining program. ARB is also incorporates a variety of other sequence analysis software. It can handle large numbers of sequences and has sophisticated tree drawing and manipulation. ARB is distributed as executables for a variety of versions of Unix, requiring that Motif be available. At the moment these are: SUN OS 4.1.x, SUN Solaris >2.4, Silicon Graphics >5.0, Linux for PC, and Digital OSF. ARB is available from its web site at http://www.mikro.biologie.tu-muenchen.de/pub/ARB/ or by ftp from ftp.mikro.biologie.tu-muenchen.de.

Tom Hall of the Department of Microbiology at North Carolina State University (tahall2@unity.ncsu.edu) has produced BioEdit, version 4.8.4. This is a sequence editor with many kinds of general molecular biology functions available (alignment, BLAST searches, plasmid drawing, restriction mapping, sequence machine trace viewing, etc.). For our purposes the feature worth mentioning is that it comes with a number of existing phylogeny programs which can be automatically run from within BioEdit. These are: Treeview, fastDNAml, and six DNA and protein programs from PHYLIP. BioEdit is available as Windows95/98/NT executables from its web site at http://www.mbio.ncsu.edu/RNaseP/info/programs/BIOEDIT/bioedit.html.

Louxin Zhang (lxzhang@krdl.org.sg) of the The Internet Bioinformatics Group of the Internet Research and Development Unit of the National University of Singapore has produced a web interface for the PHYLIP package, which can submit jobs to it. It can be obtained by e-mailing him at the above address. The interface can be used at his site as a server.

Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut@zoo.ox.ac.uk) has written Bi-De version 0.1, to simulate the evolution of trees using various models of lineage birth and death, and sampling lineages from among those extant. It can simulate branching with or without regulation of the number of lineages. It also allows the user to specify the relationship between the number of lineages and the birth rate of lineages. The program is available free for Macintoshes with system 7.0 or later, from the University of Oxford Zoology Web server at http://evolve.zoo.ox.ac.uk/Bi-De/Bi-De.html or by ftp from evolve.zoo.ox.ac.uk in directory packages as file Bi-De01b.hqx

Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut@zoo.ox.ac.uk) has written End-Epi (Endemic-Epidemic) version 1.0, a program to examine trees to assess relative cladogenesis (whether there is evidence that one clade has speciated more than another), and make lineages-through-time plots, with the objective of discovering whether the rate of speciation has been constant through time ("endemic") or has been higher initially ("epidemic"). The program is available free for Macintoshes with system 7.0 or later, from the its Web page at http://evolve.zoo.ox.ac.uk/End-Epi/End-Epi.html or by ftp from evolve.zoo.ox.ac.uk in directory packages as file End-Epi10.hqx. However the Macintosh executable will not work with operating systems later than version 7.5, unless you switch off Modern Memory Manager in the control panel first.

Paul-Michael Agapow of the Department of Biology, Imperial College, Silwood Park, U.K. (p.agapow@ic.ac.uk) has released MacroCAIC, which was developed from CAIC, by Andy Purvis and Andrew Rambaut. MacroCAIC uses phylogenies and data sets of character values to examine correlates of species richness in the phylogeny. MacroCAIC is a PowerMac and Mac binary executable. It is available from its web site at http://evolve.bio.ic.ac.uk/software/macrocaic/index.html.

Nick Grassly, currently of the Zoologisches Institut, Universität München (grassly@zi.biologie.uni-muenchen.de), has written SEQEVOLVE, a program that takes standard (Newick) formatted treefiles and evolves sequences along them following a stochastic process with the expected number and type of substitutions calculated according to a model of molecular evolution. A variety of nucleotide substitution models are implemented: Jukes and Cantor (1969), Kimura (1980), Felsenstein (1981), Hasegawa et al, (1985), and the DNAML model from PHYLIP (Felsenstein, 1995). a PowerMacintosh and Macintosh executable is available, as well as source code files for Unix systems. SEQEVOLVE does not allow for rate heterogeneity among sites or among codon positions as his more recent program Seq-Gen does. SEQEVOLVE is available by ftp from evolve.zoo.ox.ac.uk in directory packages/grassly/Seqevolve as files seqevolve-mac.hqx or seqevolve.tar.Z.

John Huelsenbeck (johnh@brahms.biology.rochester.edu) of the Department of Biology of the University of Rochester has written TheSiminator, a program that simulates the evolution of nucleotide sequences along a given tree or trees. It allows for gamma-distributed rate variation among sites, and the Hasegawa-Kishino-Yano 1985 model of nucleotide substitution. It is distributed as C source code and as a Macintosh executable, with examples of input files. It can be fetched from the Slatkin Lab's software Web page at http://ib.berkeley.edu//labs/slatkin/software.html.

Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut@zoo.ox.ac.uk) and Nick Grassly, currently of the Zoologisches Institut, Universität München ( grasslyzi.biologie.uni-muenchen.de), have written Seq-Gen (Sequence Generator), version 1.1, a program that will simulate the evolution of nucleotide sequences along a phylogeny or multiple phylogenies, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. The models available are the Hasegawa, Kishino and Yano (HKY) model, the Felsenstein F84 model, the general reversible model, the Kimura 2-parameter model and the Jukes-Cantor model. Rate heterogeneity among sites or among the different positions within a codon can be specified. A PowerMacintosh and Macintosh executable is available, as well as source code files for Unix systems. It is available from its Web page at http://evolve.zoo.ox.ac.uk/Seq-Gen/Seq-Gen.html or by ftp from evolve.zoo.ox.ac.uk in directory packages/Seq-Gen as files Seq-Gen10.hqx or Seq-Gen10.tar.Z.

Nick Grassly (currently of the Zoologisches Institut, Universität München) and Andrew Rambaut of the Department of Zoology, University of Oxford, (grassly@zi.biologie.uni-muenchen.de and andrew.rambaut@zoo.ox.ac.uk) have written PSeq-Gen (Protein-Sequence Generator), version 1.0, which will simulate the evolution of protein sequences along evolutionary trees. Three common models of amino acid substitution are implemented (PAM, JTT, and mREV), allow for user-defined amino acid frequencies. Site-specific rate heterogeneity following a gamma distribution is allowed. The program can handle multiple trees and produce multiple data sets. PSeq-Gen is available from its Web site at http://evolve.zoo.ox.ac.uk/PSeq-Gen/PSeq-Gen.html as Unix source code and also as PowerMac executables. An online manual can also be viewed at that site.

Nick Grassly (grassly@zi.biologie.uni-muenchen.de of the Zoologisches Institut, Universität München and Andrew Rambaut, of the Department of Zoology, University of Oxford have released Treevolve, version 1.32 and also Ptreevolve, programs that simulate the evolution of DNA and protein sequences respectively. The molecular sequences are simulated under coalescent models with constant population size, or with exponential population size growth. In addition different levels of recombination can be specified. In Treevolve, it is also possible to have an island model of population subdivision. Treevolve and Ptreevolve are written in ANSI C and should compile on most UNIX systems and workstations. They will also compile using Metrowerks Codewarrior on the Apple Macintosh; a project file and compiled 'fat' executable are included in the Macintosh archive. They can be obtained, and the manual of the programs viewed, from their Web site http://evolve.zoo.ox.ac.uk/Treevolve/treevolve.html. They can also be obtained by anonymous ftp from evolve.zoo.ox.ac.uk in directories packages/Treevolve or packages/Ptreevolve as compressed tar archives (for the Unix source code version) or Binhexed archives for the Macintosh executables and sources.

Jens Stoye1, Dirk Evers and Folker Meyer of the Research Center for Interdisciplinary Studies on Structure Formation (FSPM) and the Technische Fakultat of the Univeristy of Bielefeld, Germany (j.stoye@dkfz-heidelberg.de, dirk@TechFak.Uni-Bielefeld.de, and folker@TechFak.Uni-Bielefeld.de) have released ROSE, the Random model Of Sequence Evolution, version 1.0.1. It simulates the evolution of DNA, RNA, or protein sequences on a randomly generated tree, allowing for the possibility of insertions and deletions as well. It can also use a predefined tree that is input in standard format. It can report ancestral sequences or sequences at the tips of the tree, and it also keeps a record of the true multiple sequence alignment for comparison with the results of multiple sequence alignment programs. ROSE is described in the paper: Stoye, J. D. Evers and F. Meyer. 1998. Rose: generating sequence families. Bioinformatics 14: 157-163. ROSE is available in source code at its web site at http://bibiserv.TechFak.Uni-Bielefeld.DE/cgi-bin/bibi_download?tool=rose. Version 1.0 is available as binary executables for SunOS and for SGI Unix by anonymous ftp from ftp.Uni-Bielefeld.de in directory pub/projects/techfak/pi/rose/. ROSE is also available as a server.

Dmitry Filatov, of the Institute of Cell, Animal, and Population Biology of the University of Edinburgh (Dmitry.Filatov@ed.ac.uk) has released ProSeq (PROcessor of SEQuences) version 2.4. ProSeq is a sequence-editing environment that can do sequence alignment editing, translation, detection of polymorphic sites, and a variety of tests, many of a population-genetic nature, for neutrality and recombination. The part of its capabilities that are relevant to this listing is that it can simulate the evolution of a set of DNA sequences along a coalescent tree, with or without recombination. ProSeq is a Windows 95/98/NT program available from its web site at http://helios.bto.ed.ac.uk/evolgen/filatov/proseq.html.

John Huelsenbeck (johnh@brahms.biology.rochester.edu) of the Department of Biology of the University of Rochester has written StratCon, a program to test the consistency of a tree with stratigraphy of the species. It uses a permutation test described in the paper Huelsenbeck, J. 1994. Measuring and testing the fit of the stratigraphic record to phylogenetic trees. Paleobiology 20: 470-483. The program is available as a Macintosh executable. It can be fetched from the Slatkin Lab's software Web page at http://ib.berkeley.edu//labs/slatkin/software.html.

Andrew Rambaut (andrew.rambaut@zoo.ox.ac.uk) of the Department of Zoology, University of Oxford, has released QDate version 1.1. QDate estimates the date of divergence between two pairs of sequences given that the date of divergence of the members of each pairs is known. It analyzes the data under three models: (1) a perfectly clocklike model, (2) a model in which one pair has a different rate of divergence than the other, and (3) a model in which all branches have different rates. The method is described in the paper: Rambaut, A., and L. Bromham. 1998. Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15: 442-. QDate is available from its web site at http://evolve.zoo.ox.ac.uk/QDate/QDate.html. It is available as C source code for Unix or as a Macintosh executable.

Andrew Rambaut, of the Department of Zoology, University of Oxford (andrew.rambaut@zoo.ox.ac.uk) has written TipDate version 1.01. TipDate is an application for estimating the rate molecular evolution (and hence a time-scale) for a phylogeny consisting of dated tips. These will most frequently be from viruses or other fast-evolving pathogens that have been isolated over a range of dates. The program can also return the likelihood for the simple molecular clock model (i.e., assuming that all sequences are contemporary) or the non-clock model. These are useful for likelihood ratio tests of the fit of the model to the data. TipDate is available as PowerMac or Windows executables and as source code for Unix from its web site at http://evolve.zoo.ox.ac.uk/TipDate/TipDate.html.

Emmanuel Paradis, now of the Department of Biological Sciences of the University of East Anglia (E.Paradis@uea.ac.uk) released, when he was at the Institut des Sciences de l'Evolution de Montpellier, DIVERSI, a program for the analysis of diversification using phylogenetic data. It uses several methods to estimate and test for variations in diversification rates using phylogenetic data, including tests for temporal or among-clade variations in diversification rates using a maximum likelihood method. The program takes divergence times as its input. The tests are described in a paper: Paradis, E. 1997. Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing. Proceedings of the Royal Society of London B 264: 1141-1147. It is available as FORTRAN source code and also as a DOS executable, by ftp from evol.isem.univ-montp2.fr in directory /pub/pc/Log-manu.

Marc Robinson-Rechavi, of the Laboratoire de Biologie Moléculaire et Cellulaire of the École Normale Supérieure de Lyon, France (marc.robinson@ens-lyon.fr) has written RRTree, (Relative Rate tests within a Tree), version 1.1. It carries out relative rate tests for equality of evolutionary rates in DNA or protein sequences between lineages, taking into account the structure of the tree, which can be input in a number of common formats. In addition sequences are read in. The methods are described in a paper: Robinson, M., M. Gouy, C. Gautier, and D. Mouchiroud. 1998. Sensitivity of the relative-rate test to taxonomic sampling, Molecular Biology and Evolution 15: 1091-1098. RRtree is available as C source code and as executables for Windows, PowerMac, and SGI or Solaris Unix systems from its web page at http://pbil.univ-lyon1.fr/software/rrtree.html or by anonymous ftp from ftp://pbil.univ-lyon1.fr in directory /pub/mol_phylogeny/rrtree/

Mike Maciukenas, at the Department of Microbiology of the University of Illinois, has written a wonderful X-windows based interactive tree-plotting program called TreeTool. It takes as input a PHYLIP tree file, with branch lengths if they are provided, displays the tree in either rooted or unrooted form on any X-windows screen, and allows the user to modify the form of the tree and the placement of nodes and labels. When the tree is in final form the user can have it written to a Postscript file and/or printed to a Postscript- compatible printer. TreeTool is free as a C program for X windows using the Xview library. However, Xview seems to be available mostly on Sun workstations. TreeTool is available by Web from http://www.cme.msu.edu/RDP/cgis/aftpdir_show.cgi?ftpdir=pub/RDP/programs/TreeTool&title=Phylogenetic%20tree%20editor%20(TreeTool;%20Unix;%20C)&showdir=yes You can ftp the current treetool version 2.0.2 with source from rdp.life.uiuc.edu, from directory pub/RDP/programs/TreeTool. It will also be found in directory molbio/unix/treetool at iubio.bio.indiana.edu. It is also included in the GDE 2.0 sequence analysis environment mentioned above. A Debian Linux package for Intel-compatible processors is available at its web page at http://www.debian.org/Packages/unstable/x11/treetool.html. It has links to the Debian package for Xview.

Rod Page of the University of Glasgow, Scotland (dpage@udcf.gla.ac.uk), has written TreeView, a program for displaying trees on Apple Macs and Windows PCs. It can draw rooted and unrooted trees, display bootstrap values, and supports the native font and graphics file formats of both Macs and PCs. The program reads NEXUS, PHYLIP, and Hennig86 style tree files (including files produced by fastDNAml and CLUSTALW), and can save trees in the same formats so that it can convert trees among these formats. The Mac and Windows versions have almost identical interfaces. They can support the standard TrueType and Postscript fonts available on Macs and PCs, and they support the standard PICT and Windows Metafile formats for output, allowing tree pictures to be copied into other applications, as well as being saved in files. There is a MacClade/COMPONENT-style interactive tree editor and tree descriptions can be pasted directly into the program. There is a print preview and drag-and-drop facilities. Currently (version 1.5) TreeView can read up to 100 trees with up to 500 taxa. The program is free, and can be obtained by World Wide Web from http://taxonomy.zoology.gla.ac.uk/rod/treeview.html. It comes in 68K Mac, PowerMac, and Windows 95/NT executable versions (and in a Windows 3.1 executable for version 1.4). There is also online help including an online manual.

Manolo Gouy of the University of Lyon, France (mgouy@biomserv.univ-lyon1.fr), has produced NJplot, which plots rooted phylogenies (input in the standard form) and saves the plots as Postscript (for Macintosh, PICT) files. It displays branch lengths and bootstrap information (if present) and allows the user to swap branches and change the position of the root. It is described in the paper Perrière, G. and M. Gouy 1996. WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364-369. It is available free as executables for Macintosh, Windows3.1, Windows95, SunOS, SGI, IBM Unix, Linux and DEC Alpha, and as source code in C. It can be retrieved using its web page at http://pbil.univ-lyon1.fr/software/njplot.html. A Debian Linux package is available from its web page at http://www.debian.org/Packages/unstable/x11/njplot.html. It has links to a number of other Debian packages that are needed to run it, including Lesstif and the NCBI Vibrant toolkit.

Manolo Gouy of the University of Lyon, France (mgouy@biomserv.univ-lyon1.fr), has written unrooted, which draws unrooted phylogenies and saves them in Postscript files (for Macintosh, PICT files). It is available free as executables for Macintosh, Windows95, SunOS, Sun Solaris, SGI, IBM Unix, Linux and DEC Alpha, and as source code in C. It can be retrieved using its web page at http://pbil.univ-lyon1.fr/software/unrooted.html (the Windows95 and Linux executables are not listed on the web page but may be accessed through the ftp link on that page, which accesses the ftp server at pbil.univ-lyon1.fr in directory pub/mol_phylogeny/njplot/.

Tadashi Imanishi (timanish@genes.nig.ac.jp) of the National Institute of Genetics. Mishima, Japan has produced DendroMaker, version 4.1, Macintosh or PowerMacintosh programs which can draw trees on the screen and print them in Postscript files or MacPaint files. They read the trees in from tree files produced by the Neighbor-Joining or UPGMA options of the Oden package, and can also read standard Newick-format tree files. They can them edit them and reroot them in a variety of ways. They can produce PICT files of the trees. DendroMaker is distributed as several Macintosh binaries or PowerMacintosh binaries (each available in both English and Japanese versions) from its web page at http://www.cib.nig.ac.jp/dda/timanish/dendromaker/home.html. and by anonymous ftp from ftp.nig.ac.jp in directory pub/mac/bio/dendromaker.

Don Gilbert (gilbertd@bio.indiana.edu) of the Department of Biology of the University of Indiana, has written Tree Draw Deck, a Hypercard deck that draws trees on the screen from standard Newick-format tree files. The deck, which runs on Macintoshes or PowerMacs that have Hypercard Player, is based on two programs, Drawtree and Drawgram, from the 3.3 version of PHYLIP. It allows mouse-driven interactive display of the trees with selection of options for display, and allows the resulting plot to to cut into the system clipboard and pasted into drawing programs such as MacDraw or Canvas. Its printing and file-saving options do not at present work, but the clipboard method works. It is available by anonymous ftp from ftp.bio.indiana.edu in directory molbio, from ftp.ebi.ac.ukin directory pub/software/mac, and by ftp from ftp.pasteur.fr in directory pub/GenSoft/Macintosh/evolution/. A Macintosh version is available from a web page at http://yeamob.pci.chemie.uni-tuebingen.de/AAA/AAA-Tree.html by Kai-Uwe Frölich of Tübingen, Germany.

Don Gilbert (gilbertd@bio.indiana.edu) of the Department of Biology of the University of Indiana, has written Phylodendron version 0.8d, a Java application for drawing phylogenetic trees. It will read tree data in standard Newick format, then display graphical views of the phylogenetic tree. Various F options allow you to modify, adorn and edit the tree. Standard application functions to save, print, edit and manage preferences are included. This program will not estimate nor produce the tree data. Phylodendron is written as a Java application. This means that it will run on most personal computers and workstations as a standard program. This application is an enhancement of the Mac Hypercard program Tree Draw Deck released by the author in 1990, and uses tree drawing algorithms from PHYLIP. Phylodendron is available from its Web site http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/ or by anonymous ftp from iubio.bio.indiana.edu in directory molbio/java/apps/trees/. Source code is also available there.

Rick Ree of the Department of Organismic and Evolutionary Biology, Harvard University (rree@oeb.harvard.edu) has written Mavric, a package in the Python language for the manipulation and visualization of phylogenetic data. It is intended to be flexible and easily customizable to suit the needs of phylogenetic biologists who use python. Mavric is named for its core application, which aims to provide a graphical interface to phylogenies in a manner similar to MacClade. (The name Mavric is from is central application: a tool to Manipulate And Visualize RIck's Cladograms). Currently, its main usefulness is to view and manipulate phylogenetic trees. Branches can be moved around, pruned, rotated, etc. Mavric is available as Python source code from its web site at http://www.bioinformatics.org/mavric/index.html.

Andrew Rambaut (andrew.rambaut@zoo.ox.ac.uk) and Mike Charleston, both of the Department of Zoology, University of Oxford have produced the TreeEdit Phylogenetic Tree Editor version 1.0 alpha3-47. TreeEdit is an application for organizing, manipulating and viewing sets of trees. It is intended as a tool for preparing sets of trees for use in phylogeny packages. It can read and write trees in standard formats (PHYLIP, NEXUS, and CAIC). It allows drag-and-drop editing of branches, cut and paste of trees between windows (as NEXUS text), rerooting by clicking on branches, editing species labels, rotating branch order at polytomies, including and excluding species, and many other interactive features. TreeEdit is available as a PowerMac executable for MacOS System 8 or later at its web site at http://evolve.zoo.ox.ac.uk/software/TreeEdit/main.html.

Dmitri Yu. Sherbakov of the Laboratory of Molecular Systematics, Limnological Institute, Russian Academy of Sciences, Irkutsk (dysh@sherb.lin.irk.ru) has written UO (User Option), a tree-making utility for Linux and similar Unixes which allows the user to write Newick standard treefiles manually. It gets species names from a sequence file in Sequential PHYLIP format with up tp 150 sequences, then allows you to build multiple trees by clicking on species names. It allows multifurcations. UO is distributed as C sources and Linux binaries from its web page at http://sherb.lin.irk.ru/uo.html. It requires X windows and the XForms library.

Steven Brewer (Steven.Brewer@wmich.edu) and Robert Hafner of Western Michigan University have developed Phylogenetic Investigator, a teaching program that allows students to connect together organisms from a data set provided to them, to make phylogenies and examine them. The program is written as a Supercard 2.0 stack for Macintosh and PowerMacintosh systems; it is also available as a 680x0 Macintosh or PowerMac standalone executable. Version 1.6 was the last freeware version. A more recent version of Phylogenetic Investigator appears in the yearly BioQUEST Library CDROM from the BioQUEST consortium, (whose web page is at http://bioquest.org), a nonprofit publisher of interesting biological teaching software. It is listed on one ofthe BioQuest web pages (at http://www.apnet.com/bioquest/review.htm) as one of the new programs that have received a favorable initial review and are being released for use, and are candidates for inclusion in the core of the BioQuest teaching programs. It is not free; the cost of the CDROM with an individual license for one year is $99 but for that you get many different teaching programs. Site licenses for the BIOQUEST Library are $650 for single academic departments or institutions and $350 for secondary schools and secondary school districts.