# HG changeset patch # User dereeper # Date 1350474569 14400 # Node ID bbd4361b365e8e0e4468d1b3b0ef7fb92e66afd5 Uploaded diff -r 000000000000 -r bbd4361b365e phyml.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyml.sh Wed Oct 17 07:49:29 2012 -0400 @@ -0,0 +1,13 @@ +#!/bin/bash +input_tree=$1 +output_tree=$2 +output_stat=$3 +tree_suffix=_phyml_tree.txt +stat_suffix=_phyml_stats.txt +shift 3 + +directory=`dirname $0` + +$directory/phyml_3.0 -i $input_tree $*; +mv ${input_tree}${tree_suffix} ${output_tree}; +mv ${input_tree}${stat_suffix} ${output_stat}; diff -r 000000000000 -r bbd4361b365e phyml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyml.xml Wed Oct 17 07:49:29 2012 -0400 @@ -0,0 +1,153 @@ + + , a ML tree builder + ./phyml.sh $input $output_tree $output_stats -d $datatype_condition.type -m $datatype_condition.model -v $prop_invar -s $search +#if $datatype_condition.type == "nt": + -t $datatype_condition.tstv +#end if +#if $gamma_condition.gamma == "yes": + -c $gamma_condition.categories -a $gamma_condition.shape +#else: + -c 1 +#end if +#if $support_condition.support == "sh": + -b -4 +#end if +#if $support_condition.support == "boot": + -b $support_condition.boot_number +#end if +#if $support_condition.support == "no": + -b 0 +#end if +#if $random_condition.random == "yes": + --rand_start 0 --n_rand_starts $random_condition.points +#end if + --quiet + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +**Program encapsulated in Galaxy by Southgreen** + +.. class:: infomark + +**PhyML version 3.0, 2010** + +----- + +============== + Please cite: +============== + +"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0", **Guindon S., Dufayard JF., Anisimova M., Hordijk W., Lefort V., Gascuel O.**, Systematic Biology 2010 59(3):307-321; doi:10.1093/sysbio/syq010. + +"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.", **Guindon S., Gascuel O.**, Systematic Biology, 52(5):696-704, 2003. + +----- + +=========== + Overview: +=========== + +PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been widely used (~4,000 citations in ISI Web of Science), due to its simplicity and a fair accuracy/speed compromise. In the mean time research around PhyML has continued. + +We designed an efficient algorithm to search the tree space using Subtree Pruning and Regrafting (SPR) topological moves (Hordijk and Gascuel 2005), and proposed a fast branch test based on an approximate likelihood ratio test (Anisimova and Gascuel 2006). However, these novelties were not included in the official version of PhyML, and we found that improvements were still needed in order to make them effective in some practical cases. PhyML 3.0 achieves this task. + +It implements new algorithms to search the space of tree topologies with user-defined intensity. A non-parametric, Shimodaira-Hasegawa-like branch test is also available. The program provides a number of new evolutionary models and its interface was entirely re-designed. We tested PhyML 3.0 on a large collection of real data sets to ensure that the new version is stable, ready-to-use and still reasonably fast and accurate. + +----- + +For further informations, please visite the PhyML_ website. + + +.. _PhyML: http://www.atgc-montpellier.fr/phyml/ + + + diff -r 000000000000 -r bbd4361b365e phyml_3.0 Binary file phyml_3.0 has changed