diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/phylip/Makefile | 44 | ||||
| -rw-r--r-- | biology/phylip/distinfo | 1 | ||||
| -rw-r--r-- | biology/phylip/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/phylip/pkg-descr | 45 | ||||
| -rw-r--r-- | biology/phylip/pkg-plist | 70 |
5 files changed, 161 insertions, 0 deletions
diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile new file mode 100644 index 00000000000..b7ec309be6f --- /dev/null +++ b/biology/phylip/Makefile @@ -0,0 +1,44 @@ +# New ports collection makefile for: phylip +# Date created: 4 July 2000 +# Whom: dbader@eece.unm.edu +# +# $FreeBSD$ +# + +PORTNAME= phylip +PORTVERSION= 3.5 +CATEGORIES= biology +MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ +DISTNAME= ${PORTNAME} +EXTRACT_SUFX= .tar.Z + +MAINTAINER= dbader@eece.unm.edu + +NO_WRKSUBDIR= yes + +BINARIES= clique consense contml contrast dnacomp dnadist dnainvar \ + dnaml dnamlk dnamove dnapars dnapenny dolmove dollop \ + dolpenny drawgram drawtree factor fitch gendist kitsch \ + mix move neighbor penny protdist protpars restml retree \ + seqboot +DOCFILES= README clique.doc consense.doc contchar.doc contml.doc \ + contrast.doc discrete.doc distance.doc dnacomp.doc dnadist.doc \ + dnainvar.doc dnaml.doc dnamlk.doc dnamove.doc dnapars.doc \ + dnapenny.doc dollop.doc dolmove.doc dolpenny.doc draw.doc \ + drawgram.doc drawtree.doc factor.doc fitch.doc gendist.doc \ + kitsch.doc main.doc makeinf.doc mix.doc move.doc neighbor.doc \ + penny.doc protdist.doc protml.doc protpars.doc restml.doc \ + retree.doc seqboot.doc sequence.doc + +do-install: +.for f in ${BINARIES} + ${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin +.endfor +.if !defined(NOPORTDOCS) + ${MKDIR} ${PREFIX}/share/doc/${PORTNAME} +.for f in ${DOCFILES} + ${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/share/doc/${PORTNAME} +.endfor +.endif + +.include <bsd.port.mk> diff --git a/biology/phylip/distinfo b/biology/phylip/distinfo new file mode 100644 index 00000000000..462e0c381b0 --- /dev/null +++ b/biology/phylip/distinfo @@ -0,0 +1 @@ +MD5 (phylip.tar.Z) = d437d19d82fd84c723a73b6420aae4fc diff --git a/biology/phylip/pkg-comment b/biology/phylip/pkg-comment new file mode 100644 index 00000000000..b6a5c95a716 --- /dev/null +++ b/biology/phylip/pkg-comment @@ -0,0 +1 @@ +A Phylogeny Inference Package diff --git a/biology/phylip/pkg-descr b/biology/phylip/pkg-descr new file mode 100644 index 00000000000..34988635d2f --- /dev/null +++ b/biology/phylip/pkg-descr @@ -0,0 +1,45 @@ + PHYLIP - Phylogeny Inference Package (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. 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 + DNACOMP Compatibility for DNA DNAINVAR Phylogenetic invariants + DNAML Maximum likelihood method DNAMLK DNA ML with molecular clock + DNADIST Distances from sequences PROTDIST Distances from proteins + 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 0-1 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 + DOLLOP, DOLMOVE, DOLPENNY 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 + RETREE Reroots, changes names and branch lengths, and flips trees + +There is also an Unsupported Division containing two programs, makeinf and +ProtML, which were contributed by others and are maintained by their authors. + +The package includes extensive documentation files that provide the information +necessary to use and modify the programs. + + Joe Felsenstein + joe@genetics.washington.edu + Department of Genetics + University of Washington + Box 357360 + Seattle, Washington 98195-7360, U.S.A. diff --git a/biology/phylip/pkg-plist b/biology/phylip/pkg-plist new file mode 100644 index 00000000000..9c26e88aa18 --- /dev/null +++ b/biology/phylip/pkg-plist @@ -0,0 +1,70 @@ +bin/clique +bin/consense +bin/contml +bin/contrast +bin/dnacomp +bin/dnadist +bin/dnainvar +bin/dnaml +bin/dnamlk +bin/dnamove +bin/dnapars +bin/dnapenny +bin/dollop +bin/dolmove +bin/dolpenny +bin/drawgram +bin/drawtree +bin/factor +bin/fitch +bin/gendist +bin/kitsch +bin/mix +bin/move +bin/neighbor +bin/penny +bin/protdist +bin/protpars +bin/restml +bin/retree +bin/seqboot +share/doc/phylip/README +share/doc/phylip/clique.doc +share/doc/phylip/consense.doc +share/doc/phylip/contchar.doc +share/doc/phylip/contml.doc +share/doc/phylip/contrast.doc +share/doc/phylip/discrete.doc +share/doc/phylip/distance.doc +share/doc/phylip/dnacomp.doc +share/doc/phylip/dnadist.doc +share/doc/phylip/dnainvar.doc +share/doc/phylip/dnaml.doc +share/doc/phylip/dnamlk.doc +share/doc/phylip/dnamove.doc +share/doc/phylip/dnapars.doc +share/doc/phylip/dnapenny.doc +share/doc/phylip/dollop.doc +share/doc/phylip/dolmove.doc +share/doc/phylip/dolpenny.doc +share/doc/phylip/draw.doc +share/doc/phylip/drawgram.doc +share/doc/phylip/drawtree.doc +share/doc/phylip/factor.doc +share/doc/phylip/fitch.doc +share/doc/phylip/gendist.doc +share/doc/phylip/kitsch.doc +share/doc/phylip/main.doc +share/doc/phylip/makeinf.doc +share/doc/phylip/mix.doc +share/doc/phylip/move.doc +share/doc/phylip/neighbor.doc +share/doc/phylip/penny.doc +share/doc/phylip/protdist.doc +share/doc/phylip/protml.doc +share/doc/phylip/protpars.doc +share/doc/phylip/restml.doc +share/doc/phylip/retree.doc +share/doc/phylip/seqboot.doc +share/doc/phylip/sequence.doc +@dirrm share/doc/phylip |