MetaPathways protocols

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MetaPathways specifications

Information


Unique identifier OMICS_06733
Name MetaPathways
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Perl, Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.5.2
Stability Stable
Requirements
GCC compiler, NCBI BLAST, Pathway Tools
Maintained Yes

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Documentation


Maintainer


  • person_outline Steven J. Hallam <>

Publications for MetaPathways

MetaPathways in pipelines

 (3)
2018
PMCID: 5876298
PMID: 29628913
DOI: 10.3389/fmicb.2018.00520

[…] of orthologous groups of proteins (cogs, db; tatusov et al., ), metacyc (db; caspi et al., ), and refseq (db; pruitt et al., ), transporter classification database (tcdb, db; saier et al., ), metapathways (st; konwar et al., ), raxml version 8 (st; stamatakis, ), and circos (st; krzywinski et al., ) for analyzing metagenomics, metatranscriptomics, and single genome data. a series […]

2017
PMCID: 5460018
PMID: 28561030
DOI: 10.1038/ncomms15416

[…] generated using raxml v8.2.4 with the automatic protein model assignment algorithm (protgammaauto) and 100 bootstraps., metabolic reconstruction of the recovered draft genomes was performed using metapathways v2.5 (ref. ). briefly, orfs were predicted using prodigal v2.0 (ref. ), based on a minimum nucleotide length of 60, and queried against the seed subsystems (accessed march 2013), […]

2016
PMCID: 5069762
PMID: 27822530
DOI: 10.1128/mSystems.00045-16

[…] (cps), which provide assembly size, the number of contigs, contig length distribution, and n50 values. the quality-controlled contigs reads are mapped back using bt2, annotation is completed with metapathways2, and data are binned using maxbin. r and cgviewer are used for visualization. download figure┬ás5, pdf file, 0.1 mb., our moleculo library preparation and long-hybrid-read subassembly […]


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MetaPathways in publications

 (12)
PMCID: 5876298
PMID: 29628913
DOI: 10.3389/fmicb.2018.00520

[…] of orthologous groups of proteins (cogs, db; tatusov et al., ), metacyc (db; caspi et al., ), and refseq (db; pruitt et al., ), transporter classification database (tcdb, db; saier et al., ), metapathways (st; konwar et al., ), raxml version 8 (st; stamatakis, ), and circos (st; krzywinski et al., ) for analyzing metagenomics, metatranscriptomics, and single genome data. a series […]

PMCID: 5815214
PMID: 29467820
DOI: 10.1186/s13068-018-1044-9

[…] c. pasteurianum bc1 and c. diolis dsm 15410, were selected as the representative strains for genomic comparison. circos [] and mauve [] software was used to compare the assembly differences. the metapathways software (v2.0) was further adopted to re-construct the genome-wide metabolic pathways with the following parameters: (i) orfs detection by prodigal with minimal length of 60 amino acids […]

PMCID: 5688066
PMID: 29142241
DOI: 10.1038/s41467-017-01376-9

[…] in img/m (https://img.jgi.doe.gov/cgi-bin/m/main.cgi) for the metagenomic contigs which made up the population genome bins. contigs making up marinimicrobia population genome bins were run through metapathways 2.5, to annotate open reading frames (orfs) and reconstruct metabolic pathways. as the population genome bins were constructed from multiple metagenomes they contained redundant sequence […]

PMCID: 5498476
PMID: 28729857
DOI: 10.3389/fmicb.2017.01212

[…] (99.45%), nz_aase00000000.1 (90.71%), nc_007514.1 (97.8%), nc_009337.1 (98.91%), nc_010803.1 (99.98%), nc_002932.3 (97.8%), nc_011027.1 (98.89%), and nc_007512.1(98.91%). genomes were analyzed using metapathways v2.5.1, an open source pipeline for predicting reactions and pathways using default settings (, ) and using the following databases: metacyc-v4-11-07-03 (), kyoto encyclopedia of genes […]

PMCID: 5460018
PMID: 28561030
DOI: 10.1038/ncomms15416

[…] generated using raxml v8.2.4 with the automatic protein model assignment algorithm (protgammaauto) and 100 bootstraps., metabolic reconstruction of the recovered draft genomes was performed using metapathways v2.5 (ref. ). briefly, orfs were predicted using prodigal v2.0 (ref. ), based on a minimum nucleotide length of 60, and queried against the seed subsystems (accessed march 2013), […]


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MetaPathways institution(s)
Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada

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