The Exelixis Lab (original) (raw)
AxParafit: Highly optimized and parallelized version of Parafit.
What do the Programs do?
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. We have used parallel AxParafit to carry out the largest co-evolutionary analysis to date for the paper describing the software.
Citing AxParafit & AxPcoords: When publishing results using AxParafit or AxPcoords please cite the following papers:
- 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.
- Pierre Legendre, Yves Desdevises, Eric Bazin: "A Statistical Test for Host-Parasite Coevolution", Systematic Biology 51(2):217-234, 2002.
If you also used the CopyCat tool in your analyses, please cite:
- Jan P. Meier-Kolthoff, Alexander F. Auch, Daniel H. Huson and Markus Göker: "CopyCat: cophylogenetic analysis tool", Bioinformatics 23(7):898-900, 2007.
Manual, Source Code (under GPL), and Binaries
Settings:
- 512 entries test data set (n1 = 512, n2=512, n3=503, n4=505)
- 1024 entries test data set (n1=1024, n2=1024, n3=1009, n4=1015)
Link to CopyCat version with AxParafit/AxPcoords
Some pre-compiled Binaries:
- AxParafit_linux_32 (binary for 32-bit Linux architectures, using hand optimized matrix-mult)
- AxParafit_linux_32_old (if the one above yields an error "version `GLIBC_2.4' not found" try this one)
- AxParafit_linux_32_ATLASSSE2_static (statically linked binary for 32-bit Linux machines with SSE2 instruction set, using matrix-mult from ATLAS package)
- AxParafit_linux_AMD64_ATLASSSE2_static (statically linked binary for 64-bit Linux machines with SSE2 instruction set, using matrix-mult from ATLAS package)
- AxParafit_mac (binary for MACs)
- AxParafit_mac_ATLAS (binary for MACs, using matrix-mult from ATLAS package)
- AxParafit_win.exe (binary for Windows)
- AxPcoords_linux_32_GSL (statically linked binary for 32-bit Linux architectures using GSL eigenvector/eigenvalue functions)
- AxPcoords_linux_32_GSL_old (if the one above yields an error "version `GLIBC_2.4' not found" try this one)
- AxPcoords_linux_AMD64_GSL (statically linked binary for 64-bit AMD Linux architectures using GSL eigenvector/eigenvalue functions)
- AxPcoords_mac_gsl (MAC version using GSL eigenvector/eigenvalue functions)
- AxPcoords_win_gsl_static.exe (statically linked Windows version using GSL eigenvector/eigenvalue functions)
Libraries required for compiling fast version:
Results and data from the paper: An empirical Study of Smut Fungi and their Hosts: