Path: utzoo!utgpu!news-server.csri.toronto.edu!rpi!zaphod.mps.ohio-state.edu!rphroy!ox.com!msen.com!emv From: joe@GENETICS.WASHINGTON.EDU (Joe Felsenstein) Newsgroups: comp.archives Subject: [bionet.molbio.evolution] PHYLIP 3.4 RELEASED Message-ID: <1991Jun16.174819.26204@ox.com> Date: 16 Jun 91 17:48:19 GMT Sender: emv@msen.com (Edward Vielmetti, MSEN) Reply-To: joe@GENETICS.WASHINGTON.EDU (Joe Felsenstein) Followup-To: bionet.molbio.evolution Organization: (none) Lines: 165 Approved: emv@msen.com (Edward Vielmetti, MSEN) X-Original-Date: 15 Jun 91 00:17:41 GMT X-Original-Newsgroups: bionet.molbio.evolution Archive-name: bionet/molbio/phylip/1991-06-15 Archive: evolution.genetics.washington.edu:/pub/phylip* [128.95.12.41] Original-posting-by: joe@GENETICS.WASHINGTON.EDU (Joe Felsenstein) Original-subject: PHYLIP 3.4 RELEASED Reposted-by: emv@msen.com (Edward Vielmetti, MSEN) PHYLIP 3.4 RELEASED Version 3.4 of PHYLIP, a free package of programs for inferring phylogenies from various kinds of data, was released on 14 June. Generic source code in Pascal, documentation, and PCDOS executables are available for free from me as usual on diskette, by anonymous ftp from evolution.genetics.washington.edu, by e-mail, or on tape. Below I have appended the PHYLIP general information notice which describes details of distribution. There are many changes from the previous version. Here is a summary of the major changes since version 3.3: 1. All programs now have interactive menus for the user to choose options and details of the analysis. All write results to output files and trees to tree files by default. It is no longer necessary to modify the input files to specify most options. 2. Three new programs have been added: SEQBOOT is a general bootstrapping tool allowing sequences, restriction sites patterns, morphological data, etc. to be bootstrapped. NEIGHBOR performs the Neighbor-Joining and UPGMA distance matrix methods, and can handle much larger cases than the other distance methods owing to its higher speed. CONTRAST reads in a tree and a data set and computes the contrasts between species that are needed in comparative methods. 3. Almost all programs have been changed to read in multiple data sets, so together with SEQBOOT and the consensus tree program CONSENSE this allows most kinds of analysis in the package to be bootstrapped. 4. All sequence methods now allow input data to be in either "interleaved" or "sequential" format (i.e. the PHYLIP 3.3 format or the earlier one). 5. There have been corrections and improvements in the tree-drawing programs, which can now produce output for an HP Laserjet, for PC Paintbrush .PCX format files, and for Macintosh screens. 6. SEQBOOT also allows the J.Archie/D.Faith method of permutation of species within characters to test for the absence of significant evidence of phylogenetic structure, 7. The DNA Maximum Likelihood program DNAML is now about 60% faster. 8. The restriction site maximum likelihood program RESTML now allows for the fact that the data may have been generated by use of multiple enzymes. The programs will be found in directory "pub" in the ftp area of my computer "evolution.genetics.washington.edu" (IP number 128.95.12.41) in the form of two compressed tar archives (one for sources and documents and one for PCDOS executables), and also as Zoo archives which will self-extract on PCDOS machines. We hope to have self-extracting Macintosh archives of sources and Mac executables available for ftp by 19 June 1991. I will shortly post a notice listing phylogeny packages currently available that I know about. Here is the PHYLIP information sheet with further details of distribution. ----- Joe Felsenstein, Dept. of Genetics, Univ. of Washington, Seattle, WA 98195 Internet: joe@genetics.washington.edu (IP No. 128.95.12.41) Bitnet/EARN: felsenst@uwavm UUCP: ... uw-beaver!evolution.genetics!joe --------------------------------------------------------------------------- PHYLIP - Phylogeny Inference Package (version 3.4) This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 31 programs, which carry out different algorithms on different kinds of data. The programs in the package are: ---------- Programs for molecular sequence data ---------- PROTPARS Protein parsimony DNAPARS Parsimony method for DNA DNAMOVE Interactive DNA parsimony DNAPENNY Branch and bound for DNA DNABOOT Bootstraps DNA parsimony DNACOMP Compatibility for DNA DNAINVAR Phylogenetic invariants DNAML Maximum likelihood method DNAMLK DNAML with molecular clock DNADIST Distances from sequences RESTML ML for restriction sites SEQBOOT Bootstraps sequence data sets ----------- Programs for distance matrix data ------------ FITCH Fitch-Margoliash and least-squares methods KITSCH Fitch-Margoliash and least squares methods with evolutionary clock NEIGHBOR Neighbor-joining and UPGMA methods -------- Programs for gene frequencies and continuous characters ------- CONTML Maximum likelihood method GENDIST Computes genetic distances CONTRAST Computes contrasts and correlations for comparative method studies ------------- Programs for discrete state data ----------- MIX Wagner, Camin-Sokal, and mixed parsimony criteria MOVE Interactive Wagner, C-S, mixed parsimony program PENNY Finds all most parsimonious trees by branch-and-bound BOOT Bootstrap confidence interval on mixed parsimony methods DOLLOP, DOLMOVE, DOLPENNY, DOLBOOT same as preceding four programs, but for the Dollo and polymorphism parsimony criteria CLIQUE Compatibility method FACTOR recode multistate characters ---------- Programs for plotting trees and consensus trees ------- DRAWGRAM Draws cladograms and phenograms on screens, plotters and printers DRAWTREE Draws unrooted phylogenies on screens, plotters and printers CONSENSE Majority-rule and strict consensus trees The package includes extensive documentation files that provide the information necessary to use and modify the programs. COMPATIBILITY: The programs are written in a very standard subset of Pascal, a language that is available on most computers (including microcomputers). The programs require only trivial modifications to run on most machines: for example they work with only minor modifications with Turbo Pascal, and without modifications on VAX VMS Pascal. Pascal source code is distributed in the regular version of PHYLIP: compiled object code is not. To use that version, you must have a Pascal compiler. DISKETTE DISTRIBUTION: The package is distributed in a variety of microcomputer diskette formats. You should send FORMATTED diskettes, which I will return with the package written on them. See below for how many diskettes to send. The source code of the programs on the electronic network or magnetic tape versions may of course also be moved to microcomputers and compiled there. PRECOMPILED VERSIONS: Precompiled executable programs for PCDOS systems are available from me. Specify the "PCDOS executable version" and send the number of extra diskettes indicated below. An Apple Macintosh version with precompiled code is available from me or from Willem Ellis, Instituut voor Taxonomische Zoologie, Zoologisch Museum, Universiteit van Amsterdam, Plantage Middenlaan 64, 1018DH Amsterdam, Netherlands, if you send either of us 5 800K diskettes. HOW MANY DISKETTES TO SEND: The following table shows for different PCDODS formats how many diskettes to send, and how many extra diskettes to send for the PCDOS executable version: Diskette size Density For source code For executables send in addition 3.5 inch 1.44 Mb 2 2 5.25 inch 1.2 Mb 3 2 3.5 inch 720 Kb 4 3 5.25 inch 360 Kb 8 5 Some other formats are also available. You MUST tell me EXACTLY which of these formats you need. The diskettes MUST be formatted by you before being sent to me. Sending an extra diskette may be helpful. NETWORK DISTRIBUTION: The package is also available by distribution of the files directly over electronic networks, and by anonymous ftp (including PCDOS and Macintosh executables) from evolution.genetics.washington.edu. Contact me by electronic mail for details or start by fetching file pub/phylip.read.me. TAPE DISTRIBUTION: The programs can also be distributed on a magnetic tape provided by you (which should be a small tape and need only be able to hold two megabytes). Contact me for details. POLICIES: The package is distributed free. I do not make it available or support it in South Africa. The package will be written on the diskettes or tape, which will be mailed back. They can be sent to: Joe Felsenstein Electronic mail addresses: Department of Genetics SK-50 Internet: joe@genetics.washington.edu University of Washington Bitnet/EARN: felsenst@uwavm Seattle, Washington 98195 UUCP: ... uw-beaver!evolution.genetics!joe U.S.A. -- comp.archives file verification evolution.genetics.washington.edu -rw-r--r-- 1 root 79 1008961 Jun 14 12:27 /pub/phylip.exe -rw-r--r-- 1 root 79 8601 Jun 14 12:27 /pub/phylip.read.me -rw-r--r-- 1 root 79 850997 Jun 14 12:27 /pub/phylip.tar.Z -rw-r--r-- 1 root 79 1091960 Jun 14 12:27 /pub/phylipxp.exe -rw-r--r-- 1 root 79 975023 Jun 14 12:27 /pub/phylipxp.tar.Z found phylip ok evolution.genetics.washington.edu:/pub/phylip*