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comparison iqtree.xml @ 15:70acec670c30 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 069dca328b40166c018b6a971601020b6a55bc6b
author iuc
date Tue, 21 May 2024 07:25:49 +0000
parents 24d024316465
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14:0cfb4f06d047 15:70acec670c30
423 <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/> 423 <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
424 </section> 424 </section>
425 <section name="modelling_parameters" title="Modelling Parameters"> 425 <section name="modelling_parameters" title="Modelling Parameters">
426 <section name="automatic_model" expanded="False" title="Automatic model selection"> 426 <section name="automatic_model" expanded="False" title="Automatic model selection">
427 <conditional name="cond_model" > 427 <conditional name="cond_model" >
428
429 <param name="opt_custommodel" type="select" label="Do you want to use a custom model" help="See http://www.iqtree.org/doc/Substitution-Models"> 428 <param name="opt_custommodel" type="select" label="Do you want to use a custom model" help="See http://www.iqtree.org/doc/Substitution-Models">
430 <option value="true" selected="True">Yes, I want to use a custom model</option> 429 <option value="true" selected="True">Yes, I want to use a custom model</option>
431 <option value="false">No, a custom model is not needed</option> 430 <option value="false">No, a custom model is not needed</option>
432 </param> 431 </param>
433 <when value="true"> 432 <when value="true">
772 <param name="sup_min" value="0.0" /> 771 <param name="sup_min" value="0.0" />
773 <param name="nmax" value="1000" /> 772 <param name="nmax" value="1000" />
774 <param name="bcor" value="0.99" /> 773 <param name="bcor" value="0.99" />
775 <param name="nstep" value="100" /> 774 <param name="nstep" value="100" />
776 <param name="beps" value="0.5" /> 775 <param name="beps" value="0.5" />
776 <param name="boot" value="2" />
777 <output name="iqtree"> 777 <output name="iqtree">
778 <assert_contents> 778 <assert_contents>
779 <has_text_matching expression="GTR\+F\+I(\s+((-|\d|\.)+))+" /> 779 <has_text_matching expression="GTR\+F\+I(\s+((-|\d|\.)+))+" />
780 </assert_contents> 780 </assert_contents>
781 </output> 781 </output>
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1063 * **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program IcyTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree. 1063 * **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program IcyTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree.
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1065 .. _IcyTree: https://icytree.org 1065 .. _IcyTree: https://icytree.org
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1067
1068 Reducing impact of severe model violations with UFBoot 1067 Reducing impact of severe model violations with UFBoot
1069 ------------------------------------------------------ 1068 ------------------------------------------------------
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1071 Starting with IQ-TREE version 1.6 we provide a new option **-bnni** to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. With this option UFBoot will further optimize each bootstrap tree using a hill-climbing nearest neighbor interchange (NNI) search based directly on the corresponding bootstrap alignment. 1070 Starting with IQ-TREE version 1.6 we provide a new option **-bnni** to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. With this option UFBoot will further optimize each bootstrap tree using a hill-climbing nearest neighbor interchange (NNI) search based directly on the corresponding bootstrap alignment.
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