diff options
Diffstat (limited to 'biology/puzzle')
| -rw-r--r-- | biology/puzzle/DESCR | 20 | ||||
| -rw-r--r-- | biology/puzzle/Makefile | 31 | ||||
| -rw-r--r-- | biology/puzzle/PLIST | 16 | ||||
| -rw-r--r-- | biology/puzzle/distinfo | 5 |
4 files changed, 0 insertions, 72 deletions
diff --git a/biology/puzzle/DESCR b/biology/puzzle/DESCR deleted file mode 100644 index 5909faa5f6a..00000000000 --- a/biology/puzzle/DESCR +++ /dev/null @@ -1,20 +0,0 @@ -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/Makefile b/biology/puzzle/Makefile deleted file mode 100644 index 12cce60dabb..00000000000 --- a/biology/puzzle/Makefile +++ /dev/null @@ -1,31 +0,0 @@ -# $NetBSD: Makefile,v 1.7 2006/02/05 23:08:20 joerg Exp $ - -DISTNAME= tree-puzzle-5.1 -PKGNAME= puzzle-5.1 -PKGREVISION= 1 -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://www.tree-puzzle.de/ -COMMENT= Maximum likelihood analysis of molecular sequence data - -GNU_CONFIGURE= yes - -post-install: - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/puzzle - cd ${WRKSRC}/doc && ${INSTALL_DATA} tree-puzzle.pdf \ - ${PREFIX}/share/doc/puzzle - ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/puzzle - cd ${WRKSRC}/doc && ${INSTALL_DATA} tree-puzzle.html \ - *.gif ${PREFIX}/share/doc/html/puzzle - ${INSTALL_DATA_DIR} ${PREFIX}/share/examples/puzzle - cd ${WRKSRC}/data && ${INSTALL_DATA} EF.* *.a *.n *.b \ - ${PREFIX}/share/examples/puzzle - -.include "../../parallel/mpi-ch/buildlink3.mk" -.include "../../mk/bsd.pkg.mk" diff --git a/biology/puzzle/PLIST b/biology/puzzle/PLIST deleted file mode 100644 index ff59d506049..00000000000 --- a/biology/puzzle/PLIST +++ /dev/null @@ -1,16 +0,0 @@ -@comment $NetBSD: PLIST,v 1.2 2003/05/10 23:46:15 jtb Exp $ -bin/ppuzzle -bin/puzzle -share/doc/html/puzzle/ppuzzle.gif -share/doc/html/puzzle/puzzle.gif -share/doc/html/puzzle/tree-puzzle.html -share/doc/puzzle/tree-puzzle.pdf -share/examples/puzzle/EF.3trees -share/examples/puzzle/EF.phy -share/examples/puzzle/atp6.a -share/examples/puzzle/globin.a -share/examples/puzzle/marswolf.n -share/examples/puzzle/primates.b -@dirrm share/doc/puzzle -@dirrm share/doc/html/puzzle -@dirrm share/examples/puzzle diff --git a/biology/puzzle/distinfo b/biology/puzzle/distinfo deleted file mode 100644 index af98cbb147b..00000000000 --- a/biology/puzzle/distinfo +++ /dev/null @@ -1,5 +0,0 @@ -$NetBSD: distinfo,v 1.5 2005/02/22 21:28:56 agc Exp $ - -SHA1 (tree-puzzle-5.1.tar.gz) = f55464587cd04c9afb0eb83231318d91b8614798 -RMD160 (tree-puzzle-5.1.tar.gz) = 8287cc27c5c0da181c886304ecdc0290504778d1 -Size (tree-puzzle-5.1.tar.gz) = 612216 bytes |