Here are some of the other phylogeny packages that I know about. Some of them are available over Internet from ftp server machines. If you are on Internet you should familiarize yourself with ftp and with them (see entries 6 and 7 below for more information).


David Swofford of the Laboratory of Molecular Systematics, National Museum of Natural History, Smithsonian Instition, Washington, D.C. has written PAUP (Phylogenetic Analysis Using Parsimony). It can be ordered from the Center for Biodiversity, Illinois Natural History Survey, 607 East Peabody Drive, Champaign, Illinois 61820, U.S.A.

Since December, 1985, Swofford has been distributing a precompiled executable object-code versions of PAUP for the IBM PC and other MSDOS systems. As of this writing (February, 1993) he has released version 3 (PAUP/Mac) for the Macintosh, and later hopes to release version 3 for PCDOS systems and ultimately for mainframes. The cost was $50, which will increase to $100 soon. Orders received for the Mac version will be filled but the final printed documentation will arrive later, as it is not completed yet.

PAUP 3.0 is probably the most sophisticated parsimony program. It allows multistate characters, user-defined weights on individual state transitions, Wagner, Camin-Sokal and Dollo parsimony methods, bootstrap confidence intervals, and finding all most parsimonious trees by branch-and-bound. It

also has provision for computing Lake's linear phylogenetic invariants. PAUP is (a great) many times faster than the parsimony programs in PHYLIP.


Swofford also distributes an older package of programs, BIOSYS-1, including some phylogeny estimation programs, for use with gene frequency data, with particular attention to distance methods. BIOSYS-1 is distributed on an IBM PC-formatted floppy disk. Included are precompiled versions for the IBM PC and source code for uploading to IBM, VAX/VMS, Unix, Prime and CDC mainframes and minicomputers. The price is $25.00, from the same address as PAUP. BIOSYS-2 is under development, but it is too early to anticipate a completion date.


If you have a Macintosh computer and any interest in discrete-state parsimony methods (including DNA and protein parsimony), you should definitely get MacClade. It was written by Wayne Maddison and David Maddison of the University of Arizona. All distribution is by Sinauer Associates, Sunderland Massachusetts 01375, USA. Their phone number is: (413) 665 3722, FAX: (413) 665 7292. A disk with program, help file, and example data files, plus book (which has about 100 pages of intro to phylogenetic theory, and 250 pages of program instructions), is $75 U.S. ($40 for the book alone). Site licenses also available. An earlier and less capable Version 2 (which for example cannot read nucleic acid sequences and has fewer features for discrete characters) is also available by anonymous ftp from the EMBL, Indiana and Houston molecular biology software servers. Their addresses are given below under the descriptions of TreeAlign and ClustalV. MacClade 2.1 will be found among their Mac software, as a squeezed and then binhexed file.

MacClade enables you to use the mouse-window interface to specify and rearrange phylogenies by hand, and watch the number of character steps and the distribution of states of a given character on the tree change as you do so. MacClade is positively addictive and will give you a much better feel for the tree and your data. It's the closest thing to a phylogeny video game that I have seen. It has been influential in spurring the inclusion of interaction and graphics into other phylogeny programs. (I have tried to supply this functionality in PHYLIP by incorporating the programs MOVE, DOLMOVE, and DNAMOVE, which act somewhat like MacClade). MacClade does not have a sophisticated search algorithm to find best trees: it largely relies on you to do it by hand (which is surprisingly effective), with only a local rearrangement algorithm available to improve on that tree.


J. S. Farris has produced Hennig86, a fast parsimony program including branch-and-bound search for most parsimonious trees and interactive tree rearrangement. Although complete benchmarks have not been published it is said to be faster than Swofford's PAUP; both are a great many times faster than the parsimony programs in PHYLIP. The program is distributed in executable object code only and costs $50, plus $5 mailing costs ($10 outside of of the U.S.). The user's name should be stated, as copies are personalized as a copy- protection measure. It is distributed by Arnold Kluge, Amphibians and Reptiles, Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079, U.S.A. It runs on PC-compatible microcomputers with at least 512K of RAM and needs no math coprocessor or graphics monitor. It can handle up to 180 taxa and 999 characters. An 80386 version, Hennig386, is currently being tested but no release date has yet been announced.


ClaDOS, an interactive program which allows rearrangement of trees and their evaluation, mapping of characters into them, and more, is available for PCDOS systems from Kevin Nixon, L. H. Bailey Hortorium, Cornell University, 467 Mann Library, Ithaca, New York 14853. I have been unable to get information on its cost or method of distribution.


Jotun Hein, (Institute of Genetics and Ecology, University of Aarhus, 8000 Aarhus C, Denmark) has produced TreeAlign, a multiple sequence alignment program that builds trees as it aligns DNA or protein sequences. It uses a combination of distance matrix and approximate parsimony methods. TreeAlign uses too much memory for it to run on PC's (DOS or Mac systems) but is really designed for a workstation or mainframe. It is available by anonymous ftp at the Indiana, Houston, and EMBL molecular biology software distribution sites. Their network addresses are respectively: ftp.bio.indiana.edu, ftp.bchs.uh.edu, and ftp.embl-heidelberg.de. In the Indiana archive one must enter directory molbio/align, in the Houston archive it is in directory pub/gene-server in the directories unix and vms, and on the EMBL archive it is in pub/software/unix and pub/software/vax. If you are on Internet and use molecular data it is important that you learn to use anonymous ftp and become familiar with these ftp servers.


Another multisequence alignment program that estimates trees as it aligns multiple sequences is ClustalV. An older version in PCDOS executable form was distributed previously (see below for information on how to get executables for PC or Mac for the current version). Currently it is distributed as C source code by its author, Desmond Higgins. Clustal was originally developed at Trinity College, Dublin, Ireland, but version V was done at Higgin's current address, the European Molecular Biology Laboratory, Heidelberg, Germany. Clustal V successfully compiles and runs on VAX/VMS C, Apple Macintosh Think C, MSDOS Turbo C, Decstation ULTRIX C,and Sun workstations with GNU C. It is a complete rewrite and upgrade of the Clustal package which was described by Higgins and Sharp (1989).

New features include the ability to detect read different input formats (NBRF/ PIR, Fasta, EMBL/Swissprot); align old alignments; produce phylogenetic trees after alignment (Neighbor Joining trees with a bootstrap option); write different alignment formats (Clustal, NBRF/PIR, GCG, PHYLIP); full command line interface.

The program is available by anonymous ftp at the Indiana, Houston, and EMBL molecular biology distribution sites. Their network addresses are respectively: ftp.bio.indiana.edu, ftp.bchs.uh.edu, and ftp.embl-heidelberg.de. In the Indiana archive one must enter directory molbio/align, in the Houston archive it is in directory pub/gene-server in all of the four directories dos, Mac, unix, and vms, and on the EMBL archive it is in pub/software/unix or pub/software/vax. If you are on Internet and use molecular data it is important that you learn to use anonymous ftp and become familiar with one or more of these ftp servers.

If you do not have any access to Internet, you could alternatively start by sending e-mail to Des Higgins at: higgins@EMBL-Heidelberg.DE (Internet)

If you do not have access to e-mail, send a formatted PC or MAC diskette (PLEASE state which) to:

     Des Higgins
     European Molecular Biology Laboratory
     Postfach 10.2209
     Meyerhofstrasse 1
     6900 Heidelberg
He will return the diskette with the source code and documentation. He can also include an executable image for PC's or MAC.


Gary Olsen, of the Department of Microbiology, University of Illinois, has developed a speeded-up version of my program DNAML coded in C, which he calls "fastDNAml". It achieves a number of economies and also is organized so that it can be run on parallel processors -- he and his co-workers have constructed trees of very large size on a high-speed parallel processor. The program can be compiled using the "p4" portable parallel processing toolkit. It can also be run in ordinary serial mode on workstations where it is fatser than DNAML. The C program is available by anonymous ftp from the Ribosomal Database Project at info.mcs.anl.gov in directory pub/RDP/programs/fastDNAml.


Andrey A. Zharkikh, Andrey Rzhetsky, and their co-workers in the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, Ex-USSR, have produced VOSTORG, a package of programs for alignment (both manual and automatic) and inferring phylogenies by distance methods and parsimony for molecular sequences. It runs on IBM PC- compatibles and includes some rather fancy graphics. The authors are currently in the U.S., not in Siberia, and their program is sold for about $250 by Exeter Software, 100 North Country Road, Setauket, NY 11733, USA. Their telephone number is 1-800-842-5892; Fax (516)751-3435. The programs are described in a paper by Zharkikh et. al. (1991).


MEGA (Molecular Evolutionary Genetic Analysis) is due to be released at the beginning of 1993 by Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei of the Institute of Molecular Evolutionary Genetics, 328 Mueller Lab, Pennsylvania State University, University Park, Pennsylvania 16802, U.S.A. It will be an executable program for PCDOS machines, and will be menu-driven with context- sensitive help. It will analyze data from DNA, RNA and protein sequences, and distance matrices produced from other kinds of data as well. It will include the Neighbor-Joining method distance matrix method, a branch and bound parsimony method, and bootstrapping. It will also plot trees on many kinds of printers. The program will be provided free of charge if you send one 1.2 Mb 5.25-inch or 1.44 Mb 3.5-inch floppy diskette, and will be sent as soon as it is available. Inquiries can also be made by mail to M. Nei at the above address or by electronic mail to nxm2@psuvm (Bitnet) or nxm2@psuvm.psu.edu (Internet).


James Lake will soon distribute "Evomony", a program for using the "evolutionary parsimony" (invariants) method for inferring phylogenies from DNA or RNA sequences. It runs on 286 and 386 PCDOS systems with at least 500k bytes of memory. Lake intends to distribute a PCDOS version by April 1, 1993 (his choice of date, not mine!), with a Macintosh version to follow in 1994. Both will be distributed free to scientists in this field. Exact procedures for ordering Evomony have not yet been announced. Lake's address is Department of Biology, University of California, Los Angeles, California 90024.


Rod Page has written COMPONENT, a program for PCDOS systems for comparing cladograms for use in phylogeny and biogeography studies. It has far more features for biogeographic studies (such as comparing species and area cladograms) than any other package. It runs on PCDOS 286 or 386 systems under Windows 3.0 or higher. It will be released in the very near future. Its cost will be "in the $50-$75 range", and it can be ordered from Rod Page at the Department of Botany, Natural History Museum, Cromwell Road, London SW7 5BD, U.K. His phone and fax numbers are respectively (071)-938 9068 and 9260, and his e-mail address is R.Page@natural-history-museum.imperial.ac.uk or rdp@nhm.ic.ac.uk.


David Penny (Department of Botany and Zoology, Massey University, Palmerston North, New Zealand) has been offering for free distribution several PCDOS programs, one a fast parsimony program, TurboTree. There are also two others, Hadtree which computes expected frequencies of all possible distributions of nucleotides among species, and Great Deluge, an approximate search for the most parsimonious tree by a quasi-random method. He tells me that funding exigiencies are such that he may soon have to start charging for these. His electronic mail address is dpenny@massey.ac.nz.


Walter Fitch (Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92717, U.S.A.) has a package "Molevol" available free (on receipt of an appropriate number of PCDOS formatted floppy disks) with about 20 FORTRAN programs for not only estimating trees by parsimony and distance methods but doing various other manipulations of data that might be needed such as format interconversions and searching for homology and secondary structure. They are available as FORTRAN source and/or as PCDOS executables. The FORTRAN programs will also run on Sun workstations (and probably others too, I would suspect). His electronic mail address is wfitch@daedalus.bio.uci.edu.


Kent Fiala, now of SAS Institute, has written a compatibility (clique) program, based on an earlier program written by Kent and George Estabrook. Christopher Meacham has put the latest version of CLINCH (6.2), with Kent's permission, as a self-extracting DOS archive on Jim Beach's TAXACOM fileserver, huh.harvard.edu, for anonymous FTP. The self-extracting archive is "CLINCH62.EXE" in directory /pub/software/clinch. This should be FTPed as a binary file. CLINCH62.EXE is about 150 kb. When you run it, it will expand to 14 files requiring about 280 kb. The executable program is CLINCH.EXE. Readme, documentation, sample input and output, and FORTRAN source code are included. PC-CLINCH is probably the most sophisticated compatibility analysis program. The Taxacom server, by the way, also has other material related to botanical systematics, including flora information.


Christopher Meacham (Department of Integrative Biology, 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". It is available for anonymous ftp as a PCDOS executable from the Taxacom server (huh.harvard.edu) in directory pub/mip.


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 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. Farris and Mary Mickevich earlier released a package of phylogeny programs, PHYSYS, which, at about $5,000, was extremely expensive (in my opinion, which is certainly a biased one). I am not sure whether, from whom, or under what conditions it is still available.


Fujitsu Ltd. ("a $21 billion global leader in advanced computer, telecommunications, and electronic devices") sells for $28,000 US a Fujitsu S family workstation complete with a program, SINCAIDEN, which allows "experimental researchers, even those unfamiliar with such analyses, [to] easily create phylogenetic trees in their own laboratories." The program also allows searches of the major nucleic acid sequence and protein databases (the ad I saw does not make it clear whether these databases are provided with the workstation). The methods available are UPGMA, neighbor-joining, Farris's (Distance Wagner) and the modified Farris distance matrix methods. The workstation is SPARC compatible and runs SunOS. The SYNCAIDEN program was developed by the group at the National Institute of Genetics, Japan under Dr. Takashi Gojobori. Fujitsu Ltd. may be contacted at 21-8, Nishi-Shinbashi 3- chome, Minato-ku, Tokyo 105, Japan (phone 81-3-3437-5111 ext. 2831, fax 81-3- 5472-4354), or in the U.S. at Fujitsu America Inc., 3055 Orchard Drive, San Jose, California 95134-2017 (phone 1-408-432-1300 ext. 5168, fax 1-408-434- 1045).


MUST, a package of sequence management programs, is distributed on a shareware basis by Herve Phillippe, Laboratoire de Biologie Cellulaire (URA CNRS 1134 D), Batiment 444, Universite de Paris-Sud, 91405 Orsay cedex, France. His e-mail address is: adoutte@frciti51 on Bitnet/EARN. His phone and fax numbers are respectively and MUST is available on a shareware basis ($100 registration fee if you do not send diskettes) and runs on PCDOS systems using PCDOS 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.


Steve Smith, formerly of the Harvard Genome Laboratory, has written an X-Windows interactive sequence editor, GDE (Genetic Data Environment) 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 3.4 programs. The GDE 2.0 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 anonymous ftp transfer at either at golgi.harvard.edu in directory pub/GDE2.0 and also at ftp.bio.indiana.edu in directory molbio/unix/GDE.


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 and is available for anonymous ftp from ftp.bio.indiana.edu in directory molbio/unix/GDE. It is also included in the GDE 2.0 sequence analysis environment mentioned above.

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