GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution.

ABSTRACT:

Background

Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the best fit to sequence information can be lost during this process.

Results

We describe GATC, a new algorithm for reconstructing a binary gene tree with branch length. GATC returns optimal solutions according to a measure combining both tree likelihood (according to sequence evolution) and a reconciliation score under the Duplication-Transfer-Loss (DTL) model. It can either be used to construct a gene tree from scratch or to correct trees infered by existing reconstruction method, making it highly flexible to various input dat

SUBMITTER: Noutahi E 

PROVIDER: S-EPMC5954287 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature