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37 lines
1.6 KiB
Text
37 lines
1.6 KiB
Text
Treerecs: a tree reconciliation tool
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Treerecs is an open-source (species- and gene-) tree reconciliation
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software distributed under the GNU AGPL licence. It can correct,
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rearrange and (re-)root gene trees with regard to a given species tree.
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It was designed to be both efficient and easy to install and to use.
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Features
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- Correct gene trees with regard to a reference species tree
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- Root or re-root gene trees
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- Contract gene-tree branches whose support is lower than a given
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threshold, thus creating polytomies (multifurcations) that can be
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resolved therefater
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- Sample solutions with equivalent scores
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- Produce a graphical representation of the reconciled trees
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- Supported formats
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Treerecs supports the following formats: Newick, NHX, PhyloXML,
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recPhyloXML, SVG (graphical output).
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A program that can drive Treerecs, providing a GUI is Seaview, also
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available at SBo. The SlacBuild script builds two additional programs:
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1) ALEevaluate_undated: an executable of the ALE (Amalgamated likelihood
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estimation, https://github.com/ssolo/ALE), by Szollosi GJ et al). This
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version has other mapping options and a different implementation in
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Bio++ use.
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2) genetreeEditor: a small program which provides editing of gene names
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using species names and format conversion (Newick, Nhx or PhyloXML) .
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For more information, see preprint at bioRxiv:
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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations
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Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau,
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Vincent Daubin, Simon Penel, Celine Scornavacca, Manolo Gouy, Alexandros
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Stamatakis, Eric Tannier, View ORCID ProfileDavid P. Parsons
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https://www.biorxiv.org/content/10.1101/782946v1
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