Software

A software to perform DTL species tree-gene tree reconciliations.

This program takes as input a set of trees in newick format and collapses the branches of the input trees with a bootstrap value < than the given threshold.

Run ./bootstrap for visualizing the help.

To be compiled using Bio++, version > 2.0.1.

CIC

This program takes as input a set of trees in newick format and computes the normalized CIC for each of them.

Run ./CIC for visualizing the help.

To be compiled using Bio++, version > 2.0.1.

graphDTLOnline_v004

Given a dated species tree S and a gene tree G, this program computes

the graph reconciliation for G and S, according to the combinatorial

model defined in [Celine Scornavacca, Wojciech Paprotny, Vincent Berry

and Vincent Ranwez. Representing a set of reconciliations in a compact way.

Journal of Bioinformatics and Computational Biology. 11(2013) no. 2, pp. 1250025.]

Run ./graphDTL for visualizing the help.

To be compiled using Bio++, version > 2.0.1 Boost, version 1.49.