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Main.HomePage History
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February 26, 2019, at 12:54 PM
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Source code is available here and is published under the GPL for free use and distribution.
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Source code is available here under 'Downloads' and is published under the GPL for free use and distribution.
February 25, 2019, at 10:09 PM
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These tools enable measurement of functional and structural distance between closely related organisms (ex: strains of E.coli) and between domains of life (ex: Prokaryotes and Eukaryotes).
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These tools enable measurement of functional and structural distance between closely related organisms (ex: strains of E. coli) and between domains of life (ex: Prokaryotes and Eukaryotes).
February 25, 2019, at 10:09 PM
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Written by Andrew Kettring of the Sean D. Moore lab at the University of Central Florida.
See the About page for more information!
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See the About page for more information on installation and usage.
Written by Andrew Kettring of the Sean D. Moore lab at the University of Central Florida.
February 25, 2019, at 10:08 PM
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These tools enable measurement of functional and structural distance between both closely related organisms, and between domains of life (ex: Prokaryotes and Eukaryotes).
to:
These tools enable measurement of functional and structural distance between closely related organisms (ex: strains of E.coli) and between domains of life (ex: Prokaryotes and Eukaryotes).
February 25, 2019, at 10:03 PM
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February 25, 2019, at 10:01 PM
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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)
UNDER THE HOOD
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.
REQUIREMENTS
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip to obtain packages.
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_seed module requires that SBML formatted reaction networks be pre-processed by NetSeed.
Example input data is included for all three modules.
OUTPUT
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 recommed the use of MEGA from NCBI.
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See the About page for more information!
February 25, 2019, at 09:57 PM
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INPUT
Batches of whole proteomes (.FAA), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
OUTPUT
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 recommed the use of MEGA from NCBI.
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INPUT
Batches of whole proteomes (.FAA), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
Added lines 50-56:
OUTPUT
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 recommed the use of MEGA from NCBI.
February 25, 2019, at 09:54 PM
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Written by Andrew Kettring of the Sean D. Moore lab at the University of Central Florida.
February 25, 2019, at 09:52 PM
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Source code is available here, and is published under the GPL for free use and distribution.
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Source code is available here and is published under the GPL for free use and distribution.
February 25, 2019, at 09:51 PM
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PhyloMetaProt supports parallel processing for BLAST-based operations, which are notably processor intensive.
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Parallel processing is supported for BLAST-based operations and is highly recommended.
February 25, 2019, at 09:50 PM
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PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip to obtain packages
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PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip to obtain packages.
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Example input data is included for all three modules.
February 25, 2019, at 09:49 PM
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Source code is available here, and is published under the GPL for free use and distribution.
February 25, 2019, at 09:41 PM
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-Requirements-
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython
to:
REQUIREMENTS
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython. We recommend using pip to obtain packages
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-Where to get input data-
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February 25, 2019, at 09:37 PM
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Welcome to the Phylogenomics by Metabolomics and Proteomics Tools (aka: PhyloMetaProt) homepage!
These tools enable measurement of functional and structural distance between both closely related organisms, and between domains of life (ex: Prokaryotes and Eukaryotes).
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)
INPUT
Batches of whole proteomes (.FAA), lists of metabolic pathways, or lists of metabolic dependencies (aka: "seeds") and "non-seeds".
OUTPUT
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 recommed the use of MEGA from NCBI.
UNDER THE HOOD
PhyloMetaProt is written for Python 2.7 and uses a command line interface.
PhyloMetaProt supports parallel processing for BLAST-based operations, which are notably processor intensive.
-Requirements-
PhyloMetaProt requires the installation of the Python modules: numpy, pandas, and biopython
The pairwise_prot_blast module also requires installation of NCBI's BLAST executables.
-Where to get input data-
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_seed module requires that SBML formatted reaction networks be pre-processed by NetSeed.
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