AxParafit / AxPcoords – Highly optimized and Parallelized version of Parafit / DistPCoA

AxParafit / AxPcoords

:: DESCRIPTION

AxParafit and AxPcoords are highly optimized versions of Pierre Legendre’s Parafit and DistPCoA programs for statistical analysis of host-parasite coevolution. AxParafit has also been parallelized with MPI (Message Passing Interface) for compute clusters.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 AxParafit / AxPcoords

:: MORE INFORMATION

Citation

Alexandros Stamatakis, Alexander Auch, Jan Meier-Kolthoff, Markus Göker:
AxPcoords & Parallel AxParafit: Statistical Co-Phylogenetic Analyses on Thousands of Taxa”,
BMC Bioinformatics 8:405, 2007.

PASHA 1.0.10 – Parallelized Short Read Assembly

PASHA 1.0.10

:: DESCRIPTION

PASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of both shared-memory multi-core CPUs and distributed-memory compute clusters, PASHA has demonstrated its potential to perform high-quality de-novo assembly of large genomes in reasonable time with modest computing resources. Our evaluation using three small real paired-end datasets shows that PASHA is able to produce better assemblies with comparable genome coverage and mis-assembly rates compared to three leading assemblers: Velvet, ABySS and SOAPdenovo. Moreover, PASHA achieves the fastest speed for all three datasets on a single CPU.

::DEVELOPER

Liu, Yongchao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PASHA

:: MORE INFORMATION

Citation:

Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell:
Parallelized short read assembly of large genomes using de Bruijn graphs“.
BMC Bioinformatics, 2011, 12:354

MPI-PHYLIP – Parallelizing Computationally Intensive Phylogenetic Analysis

MPI-PHYLIP

:: DESCRIPTION

MPI-PHYLIP is a modified PHYLIP package using MPI to enable large-scale phylogenetic study of protein sequences, using a statistically robust number of bootstrapped datasets, to be performed in a moderate amount of time.

::DEVELOPER

National Resource for Biomedical Supercomputing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

MPI-PHYLIP

:: MORE INFORMATION

Citation

Ropelewski AJ, Nicholas HB Jr, Gonzalez Mendez RR (2010)
MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families.
PLoS ONE 5(11): e13999. doi:10.1371/journal.pone.0013999