Locus-aware decomposition of gene trees with respect to polytomous species trees.

ABSTRACT:

Background

Horizontal gene transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values.

Results

We investigate the locus tree inference problem as a possible alternative that combines the advantages of both approaches. We present several algorithms to solve the problem in the parsimony framework. We introduce a novel tree mapping, which allows us to obtain a heuristic solution to the problems of locus tree inference and duplication classification.

Conclusions

Our approach allows f

SUBMITTER: Ciach MA 

PROVIDER: S-EPMC5985597 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature