Faster exact maximum parsimony search with XMP

W. Timothy J. White1, and Barbara R. Holland. 2011. Faster exact maximum parsimony search with XMP. Bioinformatics (2011) 27 (10): 1359-1367. doi: 10.1093/bioinformatics/btr147 First published online: March 27, 2011


Abstract

Motivation: Despite trends towards maximum likelihood and Bayesian criteria, maximum parsimony (MP) remains an important criterion for evaluating phylogenetic trees. Because exact MP search is NP-complete, the computational effort needed to find provably optimal trees skyrockets with increasing numbers of taxa, limiting analyses to around 25–30 taxa. This is, in part, because currently available programs fail to take advantage of parallelism.

Results: We present XMP, a new program for finding exact MP trees that comes in both serial and parallel versions. The serial version is faster in nearly all tests than existing software. The parallel version uses a work-stealing algorithm to scale to hundreds of CPUs on a distributed-memory multiprocessor with high efficiency. An optimized SSE2 inner loop provides additional speedup for Pentium 4 and later CPUs.

Availability: C source code and several binary versions are freely available from http://www.massey.ac.nz/~wtwhite/xmp.
The parallel version requires an MPI implementation, such as the freely available MPICH2.