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authorPetar Petrov <ppetrov@paju.oulu.fi>2012-06-28 16:30:58 -0400
committerdsomero <xgizzmo@slackbuilds.org>2012-06-28 16:30:58 -0400
commit399c06897e62b4bfe41406d7ad057a6059970651 (patch)
treef9110742306a8aff4ecc7bc4f2130978164f9750 /academic
parentb6aebc4e43e39e5b519b7d5a64ba8ec4ed2355bb (diff)
downloadslackbuilds-399c06897e62b4bfe41406d7ad057a6059970651.tar.gz
academic/PhyML: Updated for version 20120412.
Signed-off-by: dsomero <xgizzmo@slackbuilds.org>
Diffstat (limited to 'academic')
-rw-r--r--academic/PhyML/PhyML.SlackBuild10
-rw-r--r--academic/PhyML/PhyML.info8
-rw-r--r--academic/PhyML/README24
-rw-r--r--academic/PhyML/slack-desc4
4 files changed, 23 insertions, 23 deletions
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild
index 08ee51b623..0ebc5df826 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 334dc43132..0fe503141c 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 87e9b170db..b52080e622 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 be2d634abf..3b074e913c 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