Software

 

Check our brand new  DTL reconciliation software TERA!

TERA

Attention!!!  All source code on this page will be downloaded as a .pdf file. Substitute the file extension .pdf with .tar and then untar the file (wordpress does not allow archive files)

Bootstrap

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..

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