Mercurial > repos > dereeper > phyml
changeset 0:bbd4361b365e draft
Uploaded
| author | dereeper |
|---|---|
| date | Wed, 17 Oct 2012 07:49:29 -0400 |
| parents | |
| children | 9e083ac98a6d |
| files | phyml.sh phyml.xml phyml_3.0 |
| diffstat | 3 files changed, 166 insertions(+), 0 deletions(-) [+] |
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--- /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};
--- /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 @@ +<tool id="phyml1" name="PhyML" version="3.0"> + <description>, a ML tree builder</description> + <command interpreter="bash">./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 + </command> + <inputs> + <param format="phylip" name="input" type="data" label="Alignment in phylip format" help="Alignment in phylip format"/> + <conditional name="datatype_condition"> + <param type="select" name="type" label="Data type"> + <option value="nt">Nucleic acids</option> + <option value="aa">Amino acids</option> + </param> + <when value="nt"> + <param type="select" name="model" label="Evolution model"> + <option value="HKY85">HKY85</option> + <option value="JC69">JC69</option> + <option value="K80">K80</option> + <option value="F81">F81</option> + <option value="F84">F84</option> + <option value="TN93">TN93</option> + <option value="GTR">GTR</option> + </param> + <param type="text" name="tstv" help="Must be a positive integer, 'e' if you want PhyML to estimate it" value="e" label="Transition/transversion ratio" /> + </when> + <when value="aa"> + <param type="select" name="model" label="Evolution model"> + <option value="LG">LG</option> + <option value="WAG">WAG</option> + <option value="JTT">JTT</option> + <option value="MtREV">MtREV</option> + <option value="Dayhoff">Dayhoff</option> + <option value="DCMut">DCMut</option> + <option value="RtREV">RtREV</option> + <option value="CpREV">CpREV</option> + <option value="VT">VT</option> + <option value="Blosum62">Blosum62</option> + <option value="MtMam">MtMam</option> + <option value="MtArt">MtArt</option> + <option value="HIVw">HIVw</option> + <option value="HIVb">HIVb</option> + </param> + </when> + </conditional> + <conditional name="gamma_condition"> + <param type="select" name="gamma" label="Discrete gamma model"> + <option value="yes">Use a gamma model</option> + <option value="no">Don't use a gamma model</option> + </param> + <when value="yes"> + <param type="text" name="categories" help="1 significates no gamma model" value="4" label="Number of categories for the discrete gamma model" /> + <param type="text" name="shape" help="'e' if you want PhyML to estimate it" value="e" label="Shape parameter of the gamma model" /> + </when> + <when value="no"> + </when> + </conditional> + <conditional name="support_condition"> + <param type="select" name="support" label="Branch support"> + <option value="sh">SH-like aLRT</option> + <option value="boot">Bootstrap</option> + <option value="no">No branch support</option> + </param> + <when value="sh"> + </when> + <when value="boot"> + <param type="text" name="boot_number" help="Must be a positive integer" value="100" label="Number of bootstrap replicate" /> + </when> + <when value="no"> + </when> + </conditional> + <param type="text" name="prop_invar" help="0.0 to ignore this parameter, 'e' if you want PhyML to estimate it" value="0.0" label="Proportion of invariant sites" /> + <param type="select" name="search" label="Tree topology search operation"> + <option value="NNI">NNI (Nearest Neighbor Interchange)</option> + <option value="SPR">SPR (Subtree Pruning and Regraphing)</option> + <option value="BEST">Best of NNI and SPR</option> + </param> + <conditional name="random_condition"> + <param type="select" name="random" label="Random starting points"> + <option value="no">Don't add random starting points</option> + <option value="yes">Add random starting points</option> + </param> + <when value="yes"> + <param type="text" name="points" help="A number greater than 0" value="4" label="Number of random starting points" /> + </when> + <when value="no"> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output_tree" label="Newick Tree"/> + <data format="txt" name="output_stats" label="Phyml statistics output"/> + </outputs> + <help> + + +.. 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/ + </help> + +</tool>