Simplifying gene trees for easier comprehension.

ABSTRACT:

Background

In the genomic age, gene trees may contain large amounts of data making them hard to read and understand. Therefore, an automated simplification is important.

Results

We present a simplification tool for gene trees called TreeSimplifier. Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the gene tree where the evolution of a gene follows species phylogeny, and they are simplified to single leaves in the gene tree. Such a simplification may fail, for example, due to genes in the gene tree that are misplaced. In this way, misplaced genes can be identified. Optionally, our tool glosses over a limited degree of "paraphyly" in a further simplification step. In both simplification steps, species c

SUBMITTER: Lott PL 

PROVIDER: S-EPMC1473203 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature