Mercurial > repos > earlhaminst > treebest_best

comparison TreeBest_best.xml @ 7:d5105943417d draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/TreeBest commit 6e40bbe92367310e9d3ec69571d08eb49af7c0a6-dirty
author earlhaminst
date Mon, 24 Feb 2025 16:32:49 +0000
parents bc049ecd9907
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6:bc049ecd9907 7:d5105943417d
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110 The 'best' command builds the best gene tree from a species tree and a CDS alignment. The resultant tree will be bootstrapped for 100 times, reconciled with the species tree and rooted by minimizing with the number of duplications and losses. Duplications and losses are also stored in the NHX format. 110 The 'best' command builds the best gene tree from a species tree and a CDS alignment. The resultant tree will be bootstrapped for 100 times, reconciled with the species tree and rooted by minimizing with the number of duplications and losses. Duplications and losses are also stored in the NHX format.
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112 Note that TreeBeST first determines the topology of resultant tree with a complex procedure, and then performs a hundred times of resampling with an improved neighbour-joining algorithm. Branch lengths are finally estimated with the standard ML method under the HKY model. 112 Note that TreeBeST first determines the topology of resultant tree with a complex procedure, and then performs a hundred times of resampling with an improved neighbour-joining algorithm. Branch lengths are finally estimated with the standard ML method under the HKY model.
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114 .. _TreeBeST: http://treesoft.sourceforge.net/treebest.shtml 114 .. _TreeBeST: https://treesoft.sourceforge.net/treebest.shtml
115 ]]> 115 ]]>
116 </help> 116 </help>
117 <citations> 117 <citations>
118 <citation type="bibtex">@phdthesis{li2016constructing, 118 <citation type="bibtex">@phdthesis{li2016constructing,
119 author = {Li, Heng}, 119 author = {Li, Heng},