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graphDTL |
Phylogenetic reconstructionpermalink |
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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/
Céline Scornavacca
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1
Platform
Linux
Source
Yes
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PopPhyl |
Toolpermalink |
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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)
- All Galaxy-related wrappers/scripts(download)
Nicolas Galtier et al.
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1
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Linux - Windows - Mac
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Yes
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ecceTERApermalink |
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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.
C++
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