![]() |
Welcome to ftp.nluug.nl Current directory: /ftp/os/Linux/distr/salix/sbo/14.2/academic/treerecs/ |
|
Contents of README: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 |
Name Last modified Size
Parent Directory -
README 19-Sep-2020 04:00 1.6K
doinst.sh 12-Jan-2020 02:55 129
slack-desc 12-Jan-2020 02:55 892
treerecs.SlackBuild 17-Oct-2020 04:49 3.5K
treerecs.info 19-Sep-2020 04:00 314
NLUUG - Open Systems. Open Standards
Become a member
and get discounts on conferences and more, see the NLUUG website!