STAR-MP
Species Tree informed Architecture Reconstruction - Maximum Parsimony
paper | download | supplemental data

Paper

Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny
Yi-Chieh Wu, Matthew D. Rasmussen, and Manolis Kellis.
Molecular Biology and Evolution. 2012. doi: 10.1093/molbev/msr222

Address correspondence to: Yi-Chieh Wu (yjw at mit.edu) and Manolis Kellis (manoli at mit.edu)

Download

STAR-MP is a phylogenetic method for reconstructing architecture evolution based on a known species tree, extant architectures, and (reconstructed) module (domain) phylogenies.

2011.06.15
STAR-MP 1.0:       starmp-1.0.tar.gz (source code)

Requirements

Supplemental data

Analysis of 9 Drosophila genomes

In our paper, we considered domain architecture rearrangements in 9 fully sequenced Drosophila species (FlyBase May 2009 Release). We used BLAST and OrthoMCL to determine modules and modules families, and connected components to determine architecture families.

Mechanisms for domain architecture rearrangement

In addition, we considered three possible mechanisms for module rearrangement and catalogued ~9000 Drosophila genes involved in such mechanisms.

References


Last updated 03/08/13.