diff options
| -rw-r--r-- | academic/PhyML/PhyML.SlackBuild | 10 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.info | 8 | ||||
| -rw-r--r-- | academic/PhyML/README | 24 | ||||
| -rw-r--r-- | academic/PhyML/slack-desc | 4 |
4 files changed, 23 insertions, 23 deletions
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index 08ee51b623934..0ebc5df826158 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for PhyML -# Copyright 2011 Petar Petrov, ppetrov@paju.oulu.fi +# Copyright 2011-2012 Petar Petrov, ppetrov@paju.oulu.fi # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,10 +24,10 @@ # Thanks to Niels Horn for some handy modifications and corrections. -PRGNAM=PhyML -VERSION=${VERSION:-20110919} +PRGNAM=PhyML +VERSION=${VERSION:-20120412} BUILD=${BUILD:-1} -TAG=${TAG:-_SBo} +TAG=${TAG:-_SBo} SRCNAM=$(echo $PRGNAM | tr A-Z a-z) @@ -96,7 +96,7 @@ find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | gr mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - doc/$SRCNAM-manual-$VERSION.pdf AUTHORS ChangeLog COPYING INSTALL README \ + doc/$SRCNAM-manual-20120306.pdf AUTHORS ChangeLog COPYING INSTALL README \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info index 334dc4313298d..0fe503141c65c 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,10 +1,10 @@ PRGNAM="PhyML" -VERSION="20110919" +VERSION="20120412" HOMEPAGE="http://code.google.com/p/phyml/" -DOWNLOAD="http://phyml.googlecode.com/files/phyml-20110919.tar.gz" -MD5SUM="d95c73c5c03d082db21564a54978f281" +DOWNLOAD="http://phyml.googlecode.com/files/phyml-20120412.tar.gz" +MD5SUM="d2207a3d6caf633c43239a01ce70f244" DOWNLOAD_x86_64="" MD5SUM_x86_64="" MAINTAINER="Petar Petrov" EMAIL="ppetrov@paju.oulu.fi" -APPROVED="rworkman" +APPROVED="dsomero" diff --git a/academic/PhyML/README b/academic/PhyML/README index 87e9b170dbd1f..b52080e622359 100644 --- a/academic/PhyML/README +++ b/academic/PhyML/README @@ -1,16 +1,16 @@ -PhyML is a software that estimates maximum likelihood phylogenies -from alignments of nucleotide or amino acid sequences. It provides a -wide range of options that were designed to facilitate standard -phylogenetic analyses. The main strengths of PhyML lies in the large -number of substitution models coupled to various options to search -the space of phylogenetic tree topologies, going from very fast and -efficient methods to slower but generally more accurate approaches. -It also implements two methods to evaluate branch supports in a sound -statistical framework (the non-parametric bootstrap and the +PhyML is a software that estimates maximum likelihood phylogenies +from alignments of nucleotide or amino acid sequences. It provides a +wide range of options that were designed to facilitate standard +phylogenetic analyses. The main strengths of PhyML lies in the large +number of substitution models coupled to various options to search +the space of phylogenetic tree topologies, going from very fast and +efficient methods to slower but generally more accurate approaches. +It also implements two methods to evaluate branch supports in a sound +statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). For details and citation -New Algorithms and Methods to Estimate Maximum-Likelihood -Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S., -Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. +New Algorithms and Methods to Estimate Maximum-Likelihood +Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S., +Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology, 59(3):307-21, 2010. diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc index be2d634abf056..3b074e913c3a7 100644 --- a/academic/PhyML/slack-desc +++ b/academic/PhyML/slack-desc @@ -9,8 +9,8 @@ PhyML: PhyML (Phylogenetic estimation using Maximum Likelihood) PhyML: PhyML: PhyML is a software that estimates maximum likelihood phylogenies -PhyML: from alignments of nucleotide or amino acid sequences. It provides -PhyML: a wide range of options that were designed to facilitate standard +PhyML: from alignments of nucleotide or amino acid sequences. It provides a +PhyML: wide range of options that were designed to facilitate standard PhyML: phylogenetic analyses. PhyML: PhyML: References: /usr/doc/PhyML-$VERSION/References |