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graphDTL

Phylogenetic reconstruction

  

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 and Vincent Berry and Vincent Ranwez. Vol. 11, No. 2 (2013) 1250025 (19 pages) Journal of Bioinformatics and Computational Biology].

This work was partially supported by the IBC http://www.ibc-montpellier.fr/

Author(s)

Céline Scornavacca


Version

1


Platform

Linux


Source

Yes


Downloads

0


Subsections

Phylogenetic reconstruction


Tags

Bio++




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PopPhyl

Tool

  

The PopPhyl project provides a set of publicly available tools C++ code to achieve SNP and genotype calling (with home made algorithms). Also are provided wrappers to use this tools in the Galaxy platforms.

Executables tools

  • Reads2SNP C++ executable (Static compilation for 32, 64 bits Linux and binary for MacOS)(download)
  • dNdSpiNpiS C++ executable (Static compilation for 64 bits Linux)(download)
  • ORF extractor perl script (download)
Galaxy-related tools

Author(s)

Nicolas Galtier et al.


Version

1


Platform

Linux - Windows - Mac


Source

Yes


Downloads

0


Subsections

Tool - Mapping - Assembler


Tags

ISEM




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ecceTERA

ecceTERA: Tree Estimating using Reconciliation and Amalgamation
version 1.2.4, 14/09/2016
(formerly known as TERA)


Given a (dated) species tree S, a set of gene trees G, and a set of costs for gene events (duplications, transfers and losses), ecceTERA computes the score of a most parsimonious reconciliation (MPR).
Additionally, ecceTERA will also compute either:

(1) a reconciliation graph describing all reconciliations for the species tree and each tree in G, according to the combinatorial model defined in [1], as well as the median reconciliations [3] and a random reconciliation (each reconciliation is outputted along with its score and event supports supports [3]), or (2) an MPR score for the “amalgamation” of all the gene trees in G (considered as unrooted), as well as an optimal gene tree according to the combinatorial model defined in [2].


[1] Celine Scornavacca, Wojciech Paprotny and Vincent Berry and Vincent Ranwez. Journal of Bioinformatics and Computational Biology Vol. 11, No. 2 (2013), p. 1250025.
[2] Celine Scornavacca, Edwin Jacox, and Gergely Szöllősi. Joint Amalgamation of Most Parsimonious Reconciled Gene Trees. Bioinformatics (2014): btu728.
[3] Thi-Hau Nguyen, Vincent Ranwez, Vincent Berry, Celine Scornavacca. Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. PloS One Vol. 8, No. 10 (2013), p. e73667.

Langage

C++


Downloads

0




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