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PPS specifications

Information


Unique identifier OMICS_01460
Name PPS
Alternative name PhyloPythiaS
Interface Web user interface
Restrictions to use Academic or non-commercial use
Programming languages Javascript, PHP
Computer skills Basic
Stability Stable
Maintained No

Maintainer


This tool is not maintained anymore.

Publication for PhyloPythiaS

PPS citations

 (21)
library_books

Diversity of Gene Clusters for Polyketide and Nonribosomal Peptide Biosynthesis Revealed by Metagenomic Analysis of the Yellow Sea Sediment

2018
Front Microbiol
PMCID: 5835077
PMID: 29535686
DOI: 10.3389/fmicb.2018.00295

[…] sequences by primer-mapping search of the sequences as described above and used for phylogenetic tree construction (allow 4 mismatches in each primer). The taxonomy of 12 contigs was determined with PhyloPythiaS analysis and annotated with fgenesb and BlastX (Patil et al., ). All the contigs were submitted to antiSMASH for further PKS and NRPS gene cluster annotation (Weber et al., ). The 12 cont […]

call_split

Discovery of carbamate degrading enzymes by functional metagenomics

2017
PLoS One
PMCID: 5730166
PMID: 29240834
DOI: 10.1371/journal.pone.0189201
call_split See protocol

[…] ce with those of its characterized homologs and with members of the lipolytic family IV was generated with Clustal Omega.Taxonomic assignation of the metagenomic sequences was determined according to PhyloPythias analysis [] (http://phylopythias.bifo.helmholtz-hzi.de, Model type Generic 2013–800 Genera) of the nucleotide sequence of the largest contigs. Same results were obtained with minimum slic […]

library_books

Assigning ecological roles to the populations belonging to a phenanthrene degrading bacterial consortium using omic approaches

2017
PLoS One
PMCID: 5591006
PMID: 28886166
DOI: 10.1371/journal.pone.0184505

[…] Rosario (INDEAR, Argentina). Sequence data are available at the NCBI Sequence Read Archive (SRA) under accession number SRP108260. The phylogenetic affiliation of the fosmid insert was evaluated with PhylopythiaS software in the generic mode, which is a previously trained mode with publicly available prokaryotic genomes and a taxonomy available at NCBI and from compositional vectors []. Based on a […]

library_books

EnSVMB: Metagenomics Fragments Classification using Ensemble SVM and BLAST

2017
Sci Rep
PMCID: 5573435
PMID: 28842700
DOI: 10.1038/s41598-017-09947-y

[…] binary SVMs, one for each pairwise combination of two species, then it assigns a fragment to a species based on the votes aggregated from these SVMs. Different from PhyloPythia that uses binary SVMs, PhyloPythiaS, a successor of PhyloPythia, adopts a structural SVM to classify fragments.DNA of different species are not the same, but there are some similar DNA fragments from different species, espe […]

library_books

Functional metagenomics reveals novel β galactosidases not predictable from gene sequences

2017
PLoS One
PMCID: 5342196
PMID: 28273103
DOI: 10.1371/journal.pone.0172545

[…] NCBI Conserved Domain Database and analyzed with CDTree []. Protein structure was predicted with Phyre 2.0 []. Taxonomic affiliations of cosmid inserts were assigned based on compositional classifier PhyloPythiaS []. Complete sequences of metagenomic Lac+ cosmids have been deposited in GenBank with accession numbers KF255992-KF255994 and KF796593-KF796611. […]

library_books

Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

2016
Front Microbiol
PMCID: 5108811
PMID: 27895636
DOI: 10.3389/fmicb.2016.01825

[…] t is important to validate the results from genome binning, although this approach has been repeatedly employed in various studies (Brown et al., ; Emerson et al., ). We suggest that validation using PhylopythiaS is suitable for genome bins of well-documented microbial taxa, such as Pseudomonas. But for novel phyla without many available genomes in public databases, comparing to single-cell amplif […]

Citations

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PPS institution(s)
Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, Saarbrücken, Germany; Department of Algorithmic Bioinformatics, Heinrich-Heine University, Düsseldorf, Germany
PPS funding source(s)
Max-Planck society; the Heinrich-Heine University

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