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authorMichael Haro <mharo@FreeBSD.org>2001-04-02 05:10:15 +0000
committerMichael Haro <mharo@FreeBSD.org>2001-04-02 05:10:15 +0000
commit8f559847930d8291af20ddebb7a9a5cdb5d3f316 (patch)
tree4342025ba7eb8bb2cd4daa3fa611839293c5bae4 /biology
parent9917f1deeda0773d8e030d9347d2db16604ed8d2 (diff)
downloadports-8f559847930d8291af20ddebb7a9a5cdb5d3f316.tar.gz
ports-8f559847930d8291af20ddebb7a9a5cdb5d3f316.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/phylip/Makefile30
-rw-r--r--biology/phylip/distinfo2
-rw-r--r--biology/phylip/files/patch-aa11
-rw-r--r--biology/phylip/pkg-descr77
-rw-r--r--biology/phylip/pkg-plist84
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