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diff --git a/academic/treerecs/README b/academic/treerecs/README new file mode 100644 index 0000000000000..cd3794ca26fe3 --- /dev/null +++ b/academic/treerecs/README @@ -0,0 +1,30 @@ +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) . |