Mercurial > repos > leomrtns > iqtree
changeset 2:87daf702e477 draft
planemo upload
| author | leomrtns |
|---|---|
| date | Thu, 05 Sep 2019 13:14:43 -0400 |
| parents | 37e42abdce08 |
| children | a396ccf6079c |
| files | iqtree.xml iqtree_macros.xml |
| diffstat | 2 files changed, 23 insertions(+), 11 deletions(-) [+] |
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--- a/iqtree.xml Tue May 21 13:06:33 2019 -0400 +++ b/iqtree.xml Thu Sep 05 13:14:43 2019 -0400 @@ -153,6 +153,8 @@ $modelling_parameters.site_specific_frequency.fmax + + #if str($tree_parameters.tree_search.ninit) != '' -ninit '$tree_parameters.tree_search.ninit' #end if @@ -183,6 +185,7 @@ $tree_parameters.tree_search.allnni $tree_parameters.tree_search.djc +$tree_parameters.tree_search.fast ## file #if $tree_parameters.tree_search.g @@ -423,16 +426,25 @@ </section> <section name="tree_parameters" title="Tree Parameters"> <section name="tree_search" expanded="False" title="Tree search parameters"> - <param argument="-n" type="integer" optional="true" label="Skip subsequent tree search (n = 0), useful when you only want to assess the phylogenetic information of the alignment. Otherwise specify number of iterations to stop (this option overrides -nstop criterion)." /> - <param argument="-ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/> - <param argument="-ntop" type="integer" value="20" optional="true" label="Specify number of top initial parsimony trees to optimize with ML nearest neighbor interchange (NNI) search to initialize the candidate set"/> - <param argument="-nbest" type="integer" value="5" optional="true" label="Specify number of trees in the candidate set to maintain during ML tree search"/> - <param argument="-nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/> - <param argument="-sprrad" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/> - <param argument="-pers" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI"/> - <param argument="-allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/> - <param argument="-djc" type="boolean" truevalue="-djc" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/> - <param argument="-g" type="data" format="txt" optional="true" label="Specify a topological constraint tree file in NEWICK format" help="The constraint tree can be a multifurcating tree and need not to include all taxa."/> + <param argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="fast tree search mode"> + <help><![CDATA[ + <br/>Emulates fasttree. According to the documentation (see http://www.iqtree.org/doc/Command-Reference#tree-search-parameters): + <br/>"Turn on the fast tree search mode, where IQ-TREE will just construct two starting trees: maximum parsimony and BIONJ, which are then optimized + by nearest neighbor interchange (NNI). Introduced in version 1.6." + <br/> Some options below may therefore be unused (e.g. the initial number of parsimony trees...) + ]]> + </help> + </param> + <param argument="-n" type="integer" optional="true" label="Skip subsequent tree search (n = 0), useful when you only want to assess the phylogenetic information of the alignment. Otherwise specify number of iterations to stop (this option overrides -nstop criterion)." /> + <param argument="-ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/> + <param argument="-ntop" type="integer" value="20" optional="true" label="Specify number of top initial parsimony trees to optimize with ML nearest neighbor interchange (NNI) search to initialize the candidate set"/> + <param argument="-nbest" type="integer" value="5" optional="true" label="Specify number of trees in the candidate set to maintain during ML tree search"/> + <param argument="-nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/> + <param argument="-sprrad" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/> + <param argument="-pers" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI"/> + <param argument="-allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/> + <param argument="-djc" type="boolean" truevalue="-djc" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/> + <param argument="-g" type="data" format="txt" optional="true" label="Specify a topological constraint tree file in NEWICK format" help="The constraint tree can be a multifurcating tree and need not to include all taxa."/> </section> <section name="single_branch" expanded="False" title="Single branch tests"> <param argument="-alrt" type="integer" optional="true" label="Specify number of replicates (>=1000) to perform SH-like approximate likelihood ratio test (SH-aLRT) (Guindon et al., 2010)" help="If number of replicates is set to 0 (-alrt 0), then the parametric aLRT test (Anisimova and Gascuel 2006) is performed, instead of SH-aLRT."/>