PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.

ABSTRACT:

Background

Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to better understand the evolutionary history of genomes.

Results

Here we describe PhylDiag, a software that identifies statistically significant synteny blocks in pairwise comparisons of eukaryote genomes. Compared to previous methods, PhylDiag uses gene trees to define gene homologies, thus allowing gene deletions to be considered as events that may break the synteny. PhylDiag also accounts for gene orientations, blocks of tandem duplicates and lineage specific de

SUBMITTER: Lucas JM 

PROVIDER: S-EPMC4155083 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature