ABOUT
PhyloMetaProt is written for Python 2.7 and uses a command line interface.
Parallel processing is supported for BLAST-based operations and is highly recommended.
MODULES
pairwise_prot_blast - Comprehensive BLASTp distance analysis between whole proteomes
pairwise_paths - Distance analysis from metabolic pathways
pairwise_seeds - Competition and complementarity of metabolic dependencies (seeds)
REQUIREMENTS
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip2 to obtain packages. Users should check to ensure the packages are installed for Python 2.7, rather than Python 3.X.
The pairwise_prot_blast module also requires installation of NCBI's BLAST executables.
INPUT
Batches of whole proteomes (.faa), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
Proteomes can be downloaded using NCBI's WGS Browser or can supplied by the user.
The pairwise_paths module was intended for use with PathwayTools, but should also function with KEGG. Any exported list of metabolic pathways should work for input!
The pairwise_seeds module requires that SBML formatted reaction networks be pre-processed by NetSeed.
Example input data is included for all three modules.
USAGE
No installation is required to use the PhyloMetaProt modules.
Unzip the package into a desirable directory.
Place the files intended to be analyzed in the module's ./infiles/ subdirectory.
Using a command shell, navigate to the module's directory.
Run the analyses using
> python2 <module_name>.py
OUTPUT
All output files will propagate in the ./outfiles/ subdirectory.
For the pairwise_prot_blast and pairwise_paths modules, output includes distance matrices and pairwise lists of distances between each of the supplied proteomes/metabolomes in the batch. Competition and complementarity matrices are generated for seed/non-seed analyses.
For clustering and visualization of phylograms we recommend the use of MEGA from NCBI.