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Pathway Tools specifications

Information


Unique identifier OMICS_03843
Name Pathway Tools
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input format PathoLogic, DAT, FBA
Output format FLATFILE
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 19.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Pathway Tools Team <>

Publications for Pathway Tools

library_books

The Pathway Tools software

2002 Bioinformatics
PMID: 12169551
DOI: 10.1093/bioinformatics/18.suppl_1.S225

Pathway Tools in pipelines

 (14)
2017
PMCID: 5460018
PMID: 28561030
DOI: 10.1038/ncomms15416

[…] against the silva small subunit (ssu) 123 database to identify the taxonomy of recovered 16s rrna genes. annotated genomes were then used to reconstruct the metabolic network of each organism using pathway tools and the metacyc database. pathway/genome databases were created for each genome, where pathway inference was based on a set of rules used by the pathway tools prediction algorithm […]

2016
PMCID: 5023668
PMID: 27695465
DOI: 10.3389/fpls.2016.01375

[…] to the rose assembled transcripts based on the go terms annotated to their corresponding homologues in the uniprot database. biochemical pathways were predicted from the rose transcripts using the pathway tools ()., to identify differentially expressed genes, high-quality cleaned reads were aligned to rose contigs using bowtie allowing up to two mismatches. only the best alignments […]

2016
PMCID: 5133247
PMID: 27994606
DOI: 10.3389/fpls.2016.01778

[…] potato, peach and woodland strawberry. protein sequences were identified by combining a blastp clustering strategy using a list of reference proteins (supplementary table ) and information from pathway tools databases (), musacyc (), the greenphyl database () and interproscan () to confirm and complement clustering results., protein sequences were aligned with mafft version 6.717b (). […]

2016
PMCID: 5952920
PMID: 28040748
DOI: 10.1093/bib/bbw130

[…] for preparing sequence alignment/map files for variant calling in sequencing pipelines []. this hpc tool was shown to significantly outperform samtools and picard on a variety of benchmarks []., pathway tools [, ] is an example of a large bioinformatics software system written in common lisp (allegro common lisp from franz inc.). pathway tools has among the largest functionality […]

2015
PMCID: 4400442
PMID: 25883299
DOI: 10.1128/genomeA.00317-15

[…] the pgap (ncbi) pipeline (). the genome of e. aerogenes consists of a single circular chromosome (53.8% g+c content), which includes 4,191 coding genes that were arranged into 309 pathways using pathway tools (, ), 260 pseudogenes, 40 rrnas (5s, 16s, 23s), 77 trnas, and 7 noncoding rnas (ncrnas)., this e. aerogenes strain showed increased growth when exposed to dde in comparison […]


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Pathway Tools in publications

 (115)
PMCID: 5898042
PMID: 29686747
DOI: 10.1186/s40793-018-0314-2

[…] operating procedure of the integrated microbial genomes platform developed by the joint genome institute []. in addition, the genome of m. psychrotolerans hv10-m2 was submitted to blastkoala [] and pathway tools [] to be compared against the kegg [] and metacyc [] databases, respectively, for pathway predictions., the properties of the draft genome of m. psychrotolerans hv10-m2 are shown […]

PMCID: 5913662
PMID: 29635372
DOI: 10.1093/gbe/evy076

[…] using orthofinder (), aligned with muscle (), and concatenated to build a phylogenetic tree using the lg amino acid substitution model in raxml v8 (). metabolic pathways were predicted with pathway tools 21.0 () and the kyoto encyclopedia of genes and genomes (kegg) mapper function on rast 2.0. pathway holes were manually inspected to verify completeness. crispr arrays were predicted […]

PMCID: 5750592
PMID: 29257110
DOI: 10.3390/pathogens6040068

[…] using ipa with a two-tailed fisher’s exact test (p ≤ 0.05) and canonical pathway enrichment., visualization of l. monocytogenes differential expression data was performed using biocyc smarttables (pathway tools version 21.0, sri international, menlo park). gene set enrichment analysis was done using a two-tailed fisher’s exact test (p ≤ 0.05) with the pathway tools l. monocytogenes strain […]

PMCID: 5732189
PMID: 29321769
DOI: 10.3389/fmicb.2017.02462

[…] accession nc_000913) and p. salmonis (refseq accession nz_cp011849.2) were determined using orthomcl v 1.4 and inparanoid v 4.0. the second draft was generated using the pathologic component of pathway-tools software (), taking as input p. salmonis lf-89 annotated genome ()., drafts were merged and the result was manually assessed, including pathway and gene annotation curations. […]

PMCID: 5522949
PMID: 28729282
DOI: 10.1128/genomeA.01587-16

[…] 1,745 proteins, 273 are involved in carbohydrate transport and metabolism, followed by 245 with only a predicted function and 180 for amino acid transport and metabolism., metabolic mapping with pathway tools v17 () showed that the organism is capable of degrading glucose, galactose, mannose, and maltose. furthermore, 173 cazymes were identified. they enable the organism to degrade complex […]


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Pathway Tools institution(s)
Artificial Intelligence Center, SRI International, Menlo Park, CA, USA
Pathway Tools funding source(s)
Supported by grants GM75742, GM080746 and GM077678 from the National Institutes of Health.

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