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Treerecs: a tree reconciliation tool
Treerecs is an open-source (species- and gene-) tree reconciliation
software distributed under the GNU AGPL licence. It can correct,
rearrange and (re-)root gene trees with regard to a given species tree.
It was designed to be both efficient and easy to install and to use.
Features
- Correct gene trees with regard to a reference species tree
- Root or re-root gene trees
- Contract gene-tree branches whose support is lower than a given
threshold, thus creating polytomies (multifurcations) that can be
resolved therefater
- Sample solutions with equivalent scores
- Produce a graphical representation of the reconciled trees
- Supported formats
Treerecs supports the following formats: Newick, NHX, PhyloXML,
recPhyloXML, SVG (graphical output).
A program that can drive Treerecs, providing a GUI is Seaview, also
available at SBo. The SlacBuild script builds two additional programs:
1) ALEevaluate_undated: an executable of the ALE (Amalgamated likelihood
estimation, https://github.com/ssolo/ALE), by Szollosi GJ et al). This
version has other mapping options and a different implementation in
Bio++ use.
2) genetreeEditor: a small program which provides editing of gene names
using species names and format conversion (Newick, Nhx or PhyloXML) .
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