diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/phylip/Makefile | 30 | ||||
| -rw-r--r-- | biology/phylip/distinfo | 2 | ||||
| -rw-r--r-- | biology/phylip/files/patch-aa | 11 | ||||
| -rw-r--r-- | biology/phylip/pkg-descr | 77 | ||||
| -rw-r--r-- | biology/phylip/pkg-plist | 84 |
5 files changed, 110 insertions, 94 deletions
diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile index b7ec309be6f0..9d73f51e11ab 100644 --- a/biology/phylip/Makefile +++ b/biology/phylip/Makefile @@ -6,10 +6,11 @@ # PORTNAME= phylip -PORTVERSION= 3.5 +PORTVERSION= 3.6 CATEGORIES= biology -MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/ +MASTER_SITES= ftp://evolution.genetics.washington.edu/pub/phylip/phylip36/ DISTNAME= ${PORTNAME} +WRKSRC= ${WRKDIR}/${DISTNAME}/src EXTRACT_SUFX= .tar.Z MAINTAINER= dbader@eece.unm.edu @@ -19,16 +20,18 @@ 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 + mix move neighbor pars penny proml protdist protpars \ + restdist restml retree seqboot treedist +DOCFILES= clique.html consense.html contchar.html contml.html \ + contrast.html discrete.html distance.html dnacomp.html \ + dnadist.html dnainvar.html dnaml.html dnamlk.html \ + dnamove.html dnapars.html dnapenny.html dollop.html \ + dolmove.html dolpenny.html draw.html drawgram.html \ + drawtree.html factor.html fitch.html gendist.html \ + kitsch.html main.html mix.html move.html neighbor.html \ + pars.html penny.html phylip.gif proml.html protdist.html \ + protpars.html restdist.html restml.html retree.html \ + seqboot.html sequence.html treedist.html do-install: .for f in ${BINARIES} @@ -37,7 +40,8 @@ do-install: .if !defined(NOPORTDOCS) ${MKDIR} ${PREFIX}/share/doc/${PORTNAME} .for f in ${DOCFILES} - ${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/share/doc/${PORTNAME} + ${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${f} \ + ${PREFIX}/share/doc/${PORTNAME} .endfor .endif diff --git a/biology/phylip/distinfo b/biology/phylip/distinfo index 462e0c381b02..e67ac37b471f 100644 --- a/biology/phylip/distinfo +++ b/biology/phylip/distinfo @@ -1 +1 @@ -MD5 (phylip.tar.Z) = d437d19d82fd84c723a73b6420aae4fc +MD5 (phylip.tar.Z) = b705658b0de0163fe87b6416c521d98c diff --git a/biology/phylip/files/patch-aa b/biology/phylip/files/patch-aa new file mode 100644 index 000000000000..78fbe0ed4f78 --- /dev/null +++ b/biology/phylip/files/patch-aa @@ -0,0 +1,11 @@ +--- Makefile.orig Mon Mar 26 19:31:01 2001 ++++ Makefile Mon Mar 26 19:35:29 2001 +@@ -77,7 +77,7 @@ + # and here are some possible DFLAGS statements: + # + # A minimal one +-DFLAGS = -DX -lX11 ++DFLAGS = -DX -I/usr/X11R6/include + # + # A basic one for debugging + #DFLAGS = -g -DX -lX11 diff --git a/biology/phylip/pkg-descr b/biology/phylip/pkg-descr index 34988635d2fb..332989387f17 100644 --- a/biology/phylip/pkg-descr +++ b/biology/phylip/pkg-descr @@ -1,45 +1,40 @@ - PHYLIP - Phylogeny Inference Package (version 3.5) + PHYLIP - Phylogeny Inference Package (version 3.6) - 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 +PHYLIP (the PHYLogeny Inference Package) is a package of programs for +inferring phylogenies (evolutionary trees). Methods that are +available in the package include parsimony, distance matrix, and +likelihood methods, including bootstrapping and consensus trees. Data +types that can be handled include molecular sequences, gene +frequencies, restriction sites, distance matrices, and 0/1 discrete +characters. -There is also an Unsupported Division containing two programs, makeinf and -ProtML, which were contributed by others and are maintained by their authors. +The programs are controlled through a menu, which asks the users which +options they want to set, and allows them to start the +computation. The data are read into the program from a text file, +which the user can prepare using any word processor or text editor +(but it is important that this text file not be in the special format +of that word processor -- it should instead be in "flat ASCII" or +"Text Only" format). Some sequence analysis programs such as alignment +programs can write data files in the PHYLIP format. Most of the +programs look for the data in a file called "infile" -- if they do not +find this file they then ask the user to type in the file name of the +data file. -The package includes extensive documentation files that provide the information -necessary to use and modify the programs. +Output is written onto special files with names like "outfile" and +"treefile". Trees written onto "treefile" are in the Newick format, an +informal standard agreed to in 1986 by authors of a number of major +phylogeny packages. - Joe Felsenstein - joe@genetics.washington.edu - Department of Genetics - University of Washington - Box 357360 - Seattle, Washington 98195-7360, U.S.A. +PHYLIP is the most widely-distributed phylogeny package, and competes +with PAUP to be the one responsible for the largest number of +published trees. PHYLIP has been in distribution since 1980, and has +over 6,000 registered users. + + Joe Felsenstein + joe@genetics.washington.edu + Department of Genetics + University of Washington + Box 357360 + Seattle, Washington 98195-7360, U.S.A. + +WWW: http://evolution.genetics.washington.edu/phylip.html
\ No newline at end of file diff --git a/biology/phylip/pkg-plist b/biology/phylip/pkg-plist index 9c26e88aa182..a31897854516 100644 --- a/biology/phylip/pkg-plist +++ b/biology/phylip/pkg-plist @@ -22,49 +22,55 @@ bin/kitsch bin/mix bin/move bin/neighbor +bin/pars bin/penny +bin/proml bin/protdist bin/protpars +bin/restdist 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 +bin/treedist +share/doc/phylip/clique.html +share/doc/phylip/consense.html +share/doc/phylip/contchar.html +share/doc/phylip/contml.html +share/doc/phylip/contrast.html +share/doc/phylip/discrete.html +share/doc/phylip/distance.html +share/doc/phylip/dnacomp.html +share/doc/phylip/dnadist.html +share/doc/phylip/dnainvar.html +share/doc/phylip/dnaml.html +share/doc/phylip/dnamlk.html +share/doc/phylip/dnamove.html +share/doc/phylip/dnapars.html +share/doc/phylip/dnapenny.html +share/doc/phylip/dollop.html +share/doc/phylip/dolmove.html +share/doc/phylip/dolpenny.html +share/doc/phylip/draw.html +share/doc/phylip/drawgram.html +share/doc/phylip/drawtree.html +share/doc/phylip/factor.html +share/doc/phylip/fitch.html +share/doc/phylip/gendist.html +share/doc/phylip/kitsch.html +share/doc/phylip/main.html +share/doc/phylip/mix.html +share/doc/phylip/move.html +share/doc/phylip/neighbor.html +share/doc/phylip/pars.html +share/doc/phylip/penny.html +share/doc/phylip/phylip.gif +share/doc/phylip/proml.html +share/doc/phylip/protdist.html +share/doc/phylip/protpars.html +share/doc/phylip/restdist.html +share/doc/phylip/restml.html +share/doc/phylip/retree.html +share/doc/phylip/seqboot.html +share/doc/phylip/sequence.html +share/doc/phylip/treedist.html @dirrm share/doc/phylip |