DeCoLT – Lateral Gene Transfer, Rearrangement, Reconciliation

DeCoLT

:: DESCRIPTION

The software DeCoLT computes adjacencies (or any type of relation, like regulation, interaction, functional relationships) between ancestral genes from gene phylogenies reconciled with a species phylogeny according to duplications, losses and lateral gene transfer. It takes as input (1) a species tree (2) a set of extant genes (3) a set of exant adjacencies (relations) between extant genes and (4) reconciled gene trees which leaves are the extant genes.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

DeCoLT

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 15:S4. doi: 10.1186/1471-2105-14-S15-S4. Epub 2013 Oct 15.
Lateral gene transfer, rearrangement, reconciliation.
Patterson M, Szöllősi G, Daubin V, Tannier E.

Prunier 2.1 – Detecting Lateral Gene Transfers by Statistical Reconciliation of Phylogenetic Forests

Prunier 2.1

:: DESCRIPTION

Prunier is a greedy algorithm to reconcile a gene tree and a species tree under an Subtree Pruning algorithm, which is considered a good model for lateral gene transfer (LGT). Its philosophy is to try to remove one after the other those parts of the tree (subtrees) that are responsible for the highest conflict. Sometimes however, in complex LGT scenarii, it is necessary to remove several independent parts of the tree to eliminate a single conflicting branch. In such cases, the first implementation of Prunier could fail at finding a good LGT scenario, and typically inferred very high numbers of LGT, most of them explaining only statistically unsupported conflict

::DEVELOPER

Sophie S Abby

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Prunier

:: MORE INFORMATION

Citation

Abby S.S., Tannier E., Gouy M. and Daubin V.
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.
BMC Bioinformatics 2010, 11:324