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Adding phylip version 3.5.
This is a FREE package of programs for inferring phylogenies and carrying out certain related tasks. At present it contains 30 programs, which carry out different algorithms on different kinds of data. PR: 19705 Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
This commit is contained in:
Steve Price
parent
54c8d2b706
commit
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Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=30408
44
biology/phylip/Makefile
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44
biology/phylip/Makefile
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# New ports collection makefile for: phylip
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# Date created: 4 July 2000
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# Whom: dbader@eece.unm.edu
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#
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# $FreeBSD$
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#
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PORTNAME= phylip
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PORTVERSION= 3.5
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CATEGORIES= biology
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MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/
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DISTNAME= ${PORTNAME}
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EXTRACT_SUFX= .tar.Z
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MAINTAINER= dbader@eece.unm.edu
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NO_WRKSUBDIR= yes
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BINARIES= clique consense contml contrast dnacomp dnadist dnainvar \
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dnaml dnamlk dnamove dnapars dnapenny dolmove dollop \
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dolpenny drawgram drawtree factor fitch gendist kitsch \
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mix move neighbor penny protdist protpars restml retree \
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seqboot
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DOCFILES= README clique.doc consense.doc contchar.doc contml.doc \
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contrast.doc discrete.doc distance.doc dnacomp.doc dnadist.doc \
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dnainvar.doc dnaml.doc dnamlk.doc dnamove.doc dnapars.doc \
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dnapenny.doc dollop.doc dolmove.doc dolpenny.doc draw.doc \
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drawgram.doc drawtree.doc factor.doc fitch.doc gendist.doc \
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kitsch.doc main.doc makeinf.doc mix.doc move.doc neighbor.doc \
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penny.doc protdist.doc protml.doc protpars.doc restml.doc \
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retree.doc seqboot.doc sequence.doc
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do-install:
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.for f in ${BINARIES}
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${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
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.endfor
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.if !defined(NOPORTDOCS)
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${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
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.for f in ${DOCFILES}
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${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/share/doc/${PORTNAME}
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.endfor
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.endif
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.include <bsd.port.mk>
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1
biology/phylip/distinfo
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1
biology/phylip/distinfo
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MD5 (phylip.tar.Z) = d437d19d82fd84c723a73b6420aae4fc
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1
biology/phylip/pkg-comment
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1
biology/phylip/pkg-comment
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A Phylogeny Inference Package
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45
biology/phylip/pkg-descr
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biology/phylip/pkg-descr
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PHYLIP - Phylogeny Inference Package (version 3.5)
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This is a FREE package of programs for inferring phylogenies and carrying
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out certain related tasks. At present it contains 30 programs, which carry out
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different algorithms on different kinds of data. The programs in the package
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are:
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---------- Programs for molecular sequence data ----------
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PROTPARS Protein parsimony DNAPARS Parsimony method for DNA
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DNAMOVE Interactive DNA parsimony DNAPENNY Branch and bound for DNA
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DNACOMP Compatibility for DNA DNAINVAR Phylogenetic invariants
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DNAML Maximum likelihood method DNAMLK DNA ML with molecular clock
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DNADIST Distances from sequences PROTDIST Distances from proteins
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RESTML ML for restriction sites SEQBOOT Bootstraps sequence data sets
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----------- Programs for distance matrix data ------------
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FITCH Fitch-Margoliash and least-squares methods
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KITSCH Fitch-Margoliash and least squares methods with evolutionary clock
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NEIGHBOR Neighbor-joining and UPGMA methods
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-------- Programs for gene frequencies and continuous characters -------
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CONTML Maximum likelihood method GENDIST Computes genetic distances
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CONTRAST Computes contrasts and correlations for comparative method studies
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------------- Programs for 0-1 discrete state data -----------
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MIX Wagner, Camin-Sokal, and mixed parsimony criteria
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MOVE Interactive Wagner, C-S, mixed parsimony program
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PENNY Finds all most parsimonious trees by branch-and-bound
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DOLLOP, DOLMOVE, DOLPENNY same as preceding four programs, but for
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the Dollo and polymorphism parsimony criteria
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CLIQUE Compatibility method FACTOR recode multistate characters
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---------- Programs for plotting trees and consensus trees -------
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DRAWGRAM Draws cladograms and phenograms on screens, plotters and printers
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DRAWTREE Draws unrooted phylogenies on screens, plotters and printers
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CONSENSE Majority-rule and strict consensus trees
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RETREE Reroots, changes names and branch lengths, and flips trees
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There is also an Unsupported Division containing two programs, makeinf and
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ProtML, which were contributed by others and are maintained by their authors.
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The package includes extensive documentation files that provide the information
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necessary to use and modify the programs.
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Joe Felsenstein
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joe@genetics.washington.edu
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Department of Genetics
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University of Washington
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Box 357360
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Seattle, Washington 98195-7360, U.S.A.
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70
biology/phylip/pkg-plist
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70
biology/phylip/pkg-plist
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bin/clique
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bin/consense
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bin/contml
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bin/contrast
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bin/dnacomp
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bin/dnadist
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bin/dnainvar
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bin/dnaml
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bin/dnamlk
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bin/dnamove
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bin/dnapars
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bin/dnapenny
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bin/dollop
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bin/dolmove
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bin/dolpenny
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bin/drawgram
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bin/drawtree
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bin/factor
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bin/fitch
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bin/gendist
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bin/kitsch
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bin/mix
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bin/move
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bin/neighbor
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bin/penny
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bin/protdist
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bin/protpars
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bin/restml
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bin/retree
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bin/seqboot
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share/doc/phylip/README
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share/doc/phylip/clique.doc
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share/doc/phylip/consense.doc
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share/doc/phylip/contchar.doc
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share/doc/phylip/contml.doc
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share/doc/phylip/contrast.doc
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share/doc/phylip/discrete.doc
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share/doc/phylip/distance.doc
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share/doc/phylip/dnacomp.doc
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share/doc/phylip/dnadist.doc
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share/doc/phylip/dnainvar.doc
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share/doc/phylip/dnaml.doc
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share/doc/phylip/dnamlk.doc
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share/doc/phylip/dnamove.doc
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share/doc/phylip/dnapars.doc
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share/doc/phylip/dnapenny.doc
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share/doc/phylip/dollop.doc
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share/doc/phylip/dolmove.doc
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share/doc/phylip/dolpenny.doc
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share/doc/phylip/draw.doc
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share/doc/phylip/drawgram.doc
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share/doc/phylip/drawtree.doc
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share/doc/phylip/factor.doc
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share/doc/phylip/fitch.doc
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share/doc/phylip/gendist.doc
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share/doc/phylip/kitsch.doc
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share/doc/phylip/main.doc
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share/doc/phylip/makeinf.doc
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share/doc/phylip/mix.doc
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share/doc/phylip/move.doc
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share/doc/phylip/neighbor.doc
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share/doc/phylip/penny.doc
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share/doc/phylip/protdist.doc
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share/doc/phylip/protml.doc
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share/doc/phylip/protpars.doc
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share/doc/phylip/restml.doc
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share/doc/phylip/retree.doc
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share/doc/phylip/seqboot.doc
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share/doc/phylip/sequence.doc
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@dirrm share/doc/phylip
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