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) . 

For more information, see preprint at  bioRxiv:
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations
Nicolas Comte, Benoit Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau,
Vincent Daubin, Simon Penel, Celine Scornavacca, Manolo Gouy, Alexandros
Stamatakis, Eric Tannier, View ORCID ProfileDavid P. Parsons
https://www.biorxiv.org/content/10.1101/782946v1