From 7bb17a24ecf6623231b63c42abdfea53dbf6f2d6 Mon Sep 17 00:00:00 2001 From: rh Date: Wed, 28 Jul 1999 19:55:17 +0000 Subject: Initial import of puzzle-4.0.2, a maximum likelihood analysis tool of molecular sequence data --- biology/puzzle/Makefile | 24 ++++++++++++++++++++++++ biology/puzzle/files/md5 | 3 +++ biology/puzzle/files/patch-sum | 5 +++++ biology/puzzle/patches/patch-aa | 20 ++++++++++++++++++++ biology/puzzle/patches/patch-ab | 13 +++++++++++++ biology/puzzle/patches/patch-ac | 22 ++++++++++++++++++++++ biology/puzzle/pkg/COMMENT | 1 + biology/puzzle/pkg/DESCR | 20 ++++++++++++++++++++ biology/puzzle/pkg/PLIST | 4 ++++ 9 files changed, 112 insertions(+) create mode 100644 biology/puzzle/Makefile create mode 100644 biology/puzzle/files/md5 create mode 100644 biology/puzzle/files/patch-sum create mode 100644 biology/puzzle/patches/patch-aa create mode 100644 biology/puzzle/patches/patch-ab create mode 100644 biology/puzzle/patches/patch-ac create mode 100644 biology/puzzle/pkg/COMMENT create mode 100644 biology/puzzle/pkg/DESCR create mode 100644 biology/puzzle/pkg/PLIST (limited to 'biology/puzzle') diff --git a/biology/puzzle/Makefile b/biology/puzzle/Makefile new file mode 100644 index 00000000000..8ca9dd8edc5 --- /dev/null +++ b/biology/puzzle/Makefile @@ -0,0 +1,24 @@ +# $NetBSD: Makefile,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $ + +DISTNAME= puzzle-402 +PKGNAME= puzzle-4.0.2 +WRKSRC= ${WRKDIR}/${PKGNAME}/src +CATEGORIES= biology +MASTER_SITES= http://members.tripod.de/korbi/puzzle/ \ + ftp://ftp.ebi.ac.uk/pub/software/unix/puzzle/ \ + ftp://ftp.pasteur.fr/pub/GenSoft/unix/evolution/Puzzle/ \ + ftp://iubio.bio.indiana.edu/molbio/evolve/puzzle/ \ + http://iubio.bio.indiana.edu/soft/molbio/evolve/puzzle/ + +MAINTAINER= babafou@babafou.eu.org +HOMEPAGE= http://members.tripod.de/korbi/puzzle/ + +MAKEFILE= makefile +ALL_TARGET= puzzle + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/puzzle ${PREFIX}/bin + ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/puzzle + ${INSTALL_DATA} ${WRKDIR}/${PKGNAME}/doc/manual.html ${PREFIX}/share/doc/puzzle + +.include "../../mk/bsd.pkg.mk" diff --git a/biology/puzzle/files/md5 b/biology/puzzle/files/md5 new file mode 100644 index 00000000000..98aa2b37ae1 --- /dev/null +++ b/biology/puzzle/files/md5 @@ -0,0 +1,3 @@ +$NetBSD: md5,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $ + +MD5 (puzzle-402.tar.gz) = 635ae0594a06a379add882c90d0c616d diff --git a/biology/puzzle/files/patch-sum b/biology/puzzle/files/patch-sum new file mode 100644 index 00000000000..6b07c229b89 --- /dev/null +++ b/biology/puzzle/files/patch-sum @@ -0,0 +1,5 @@ +$NetBSD: patch-sum,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $ + +MD5 (patch-aa) = 431dbe0506217e4b1772b4e18c839285 +MD5 (patch-ab) = bf25b9a245e28967462928076816d80a +MD5 (patch-ac) = bff9421d8ba9b763a801b2a8bd888c82 diff --git a/biology/puzzle/patches/patch-aa b/biology/puzzle/patches/patch-aa new file mode 100644 index 00000000000..921af783c37 --- /dev/null +++ b/biology/puzzle/patches/patch-aa @@ -0,0 +1,20 @@ +$NetBSD: patch-aa,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $ + +--- makefile.orig Sun May 23 15:40:28 1999 ++++ makefile Sun May 23 15:40:42 1999 +@@ -10,11 +10,11 @@ + + + # ANSI C compiler +-CC = gcc +-CFLAGS = -O3 -Wall -pedantic -ansi ++#CC = gcc ++#CFLAGS = -O3 -Wall -pedantic -ansi + # Comment out for compiler other than gcc +-#CC = cc +-#CFLAGS = -O ++CC = cc ++CFLAGS = -O + + # ANSI math library + LIBFLAGS = -lm diff --git a/biology/puzzle/patches/patch-ab b/biology/puzzle/patches/patch-ab new file mode 100644 index 00000000000..343ad02a0e3 --- /dev/null +++ b/biology/puzzle/patches/patch-ab @@ -0,0 +1,13 @@ +$NetBSD: patch-ab,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $ + +--- ml.h.orig Sun May 23 12:08:41 1999 ++++ ml.h Sun May 23 12:08:49 1999 +@@ -165,7 +165,7 @@ + /* function prototypes of all ml function */ + + void convfreq(dvector); +-void radixsort(cmatrix, ivector, int, int, int *); ++void my_radixsort(cmatrix, ivector, int, int, int *); + void condenceseq(cmatrix, ivector, cmatrix, ivector, int, int, int); + void countconstantsites(cmatrix, ivector, int, int, int *); + void evaluateseqs(void); diff --git a/biology/puzzle/patches/patch-ac b/biology/puzzle/patches/patch-ac new file mode 100644 index 00000000000..ff0797222ad --- /dev/null +++ b/biology/puzzle/patches/patch-ac @@ -0,0 +1,22 @@ +$NetBSD: patch-ac,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $ + +--- ml1.c.orig Sun May 23 12:07:15 1999 ++++ ml1.c Sun May 23 12:07:36 1999 +@@ -65,7 +65,7 @@ + } + + /* sort site patters of original input data */ +-void radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite, ++void my_radixsort(cmatrix seqchar, ivector ali, int maxspc, int maxsite, + int *numptrn) + { + int i, j, k, l, n, pass; +@@ -181,7 +181,7 @@ + + convfreq(Freqtpm); /* make all frequencies slightly different */ + ali = new_ivector(Maxsite); +- radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn); ++ my_radixsort(Seqchar, ali, Maxspc, Maxsite, &Numptrn); + Seqpat = new_cmatrix(Maxspc, Numptrn); + constpat = new_ivector(Numptrn); + Weight = new_ivector(Numptrn); diff --git a/biology/puzzle/pkg/COMMENT b/biology/puzzle/pkg/COMMENT new file mode 100644 index 00000000000..c001d039dde --- /dev/null +++ b/biology/puzzle/pkg/COMMENT @@ -0,0 +1 @@ +Maximum likelihood analysis of molecular sequence data diff --git a/biology/puzzle/pkg/DESCR b/biology/puzzle/pkg/DESCR new file mode 100644 index 00000000000..5909faa5f6a --- /dev/null +++ b/biology/puzzle/pkg/DESCR @@ -0,0 +1,20 @@ +PUZZLE is a computer program to reconstruct phylogenetic trees +from molecular sequence data by maximum likelihood. It implements +a fast tree search algorithm, quartet puzzling, that allows +analysis of large data sets and automatically assigns estimations +of support to each internal branch. PUZZLE also computes pairwise +maximum likelihood distances as well as branch lengths for user +specified trees. Branch lengths can also be calculated under the +clock-assumption. In addition, PUZZLE offers a novel method, +likelihood mapping, to investigate the support of a hypothesized +internal branch without computing an overall tree and to +visualize the phylogenetic content of a sequence alignment. +PUZZLE also conducts a number of statistical tests on the data +set (chi-square test for homogeneity of base composition, +likelihood ratio to test the clock hypothesis, Kishino-Hasegaw a +test). The models of substitution provided by PUZZLE are TN, HKY, +F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62 for +amino acids, and F81 for two-state data. Rate heterogeneity is +modelled by a discrete Gamma distribution and by allowing +invariable sites. The corresponding parameters can be inferred +from the data set. diff --git a/biology/puzzle/pkg/PLIST b/biology/puzzle/pkg/PLIST new file mode 100644 index 00000000000..3356fd35c39 --- /dev/null +++ b/biology/puzzle/pkg/PLIST @@ -0,0 +1,4 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 1999/07/28 19:55:17 rh Exp $ +bin/puzzle +share/doc/puzzle/manual.html +@dirrm share/doc/puzzle -- cgit v1.2.3