MetaPathways statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MetaPathways

Tool usage distribution map

This map represents all the scientific publications referring to MetaPathways per scientific context
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MetaPathways specifications


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
GCC compiler, NCBI BLAST, Pathway Tools
Maintained Yes


No version available



  • person_outline Steven J. Hallam

Publications for MetaPathways

MetaPathways citations


A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill

Front Microbiol
PMCID: 5876298
PMID: 29628913
DOI: 10.3389/fmicb.2018.00520

[…] lusters 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 of visual […]


Genomic comparison of Clostridium species with the potential of utilizing red algal biomass for biobutanol production

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

[…] 988, 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 […]


Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco thermodynamic gradients

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

[…] nd in IMG/M ( 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 […]


Inferring metabolic pathway activity levels from RNA Seq data

BMC Genomics
PMCID: 5009525
PMID: 27585456
DOI: 10.1186/s12864-016-2823-y

[…] iptome data, the first challenge of pathway analysis is to decide which metabolic pathways are active in the sampled community (i.e., pathway activity detection). Recent software tools (MEGAN4 [] and MetaPathways [] using SEED and KEGG (Kyoto Encyclopedia of Genes and Genomes) [] annotations) enable the organization of transcripts or reads into ortholog groups and pathways by collecting all transc […]


Moleculo Long Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

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

[…] genomes and metatranscriptomes from Kansas soils A, B, and C were trimmed to ~225 bp. Both SR and RMR, were assembled using MEGAHIT () with mixed k-mers (21 to 121 k).The contigs were annotated using MetaPathways2 as previously described (, ). Metatranscriptomes and metagenomes were mapped to assemblies and genome bins using Bowtie2 (). The gene counts per enzyme (EC number) and transcript reads p […]


Metagenomic Analysis Suggests Modern Freshwater Microbialites Harbor a Distinct Core Microbial Community

Front Microbiol
PMCID: 4729913
PMID: 26903951
DOI: 10.3389/fmicb.2015.01531
call_split See protocol

[…] stems and RefSeq databases with a minimum E-value cutoff of 10-5, a minimum percent identity cutoff of 60%, and a minimum alignment length cutoff of 50 base pairs.MetaCyc annotations were provided by MetaPathways, a modular pipeline for gene prediction and annotation that uses pathway tools and the MetaCyc database to construct environmental pathway/genome databases (ePGBDs; ). Metapathways using […]

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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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