AxParafit & AxPcoords Homepage
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.
and:
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
AxParafit Source code
AxPcoords source code
AxParafit & AxPcoords Manual
Test-Data
- 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)
AMD ACML Library
Intel MKL Library
GNU Scientific Library
ATLAS Library
Results And Data from the Paper: Empirical Study of Smut Fungi and their Hosts
Entire Archive
AxParafit Output U 99
AxParafit Output U 999
AxParafit Output U 9999
AxParafit Output W 99
AxParafit Output W 999
AxParafit Output W 9999
Host Taxonomy
Queries and Sources
Unique Associations
AxParafit Input Data U
AxParafit Input Data W