academic/treerecs: Added (a tree reconciliation tool).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

1 files changed, 30 insertions, 0 deletions

diff --git a/academic/treerecs/README b/academic/treerecs/README
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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) .