slackbuilds_ponce/academic/treerecs

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) .