PhyloPythia protocols

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PhyloPythia specifications

Information


Unique identifier OMICS_01459
Name PhyloPythia
Interface Web user interface
Restrictions to use None
Input data A multiclass support vector machine (SVM) classifier with the oligonucleotide composition of variable-length genome fragments.
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for PhyloPythia

PhyloPythia in pipeline

2016
PMCID: 4926282
PMID: 27353502
DOI: 10.1038/srep28810

[…] which was set to 150. gene finding and annotation and binning was performed following the strategy developed by campanaro et al.. taxonomy was determined using phylophlan and further refined using phylopythia software. kegg functional analysis was refined using ghostkoala (http://www.kegg.jp/ghostkoala/). reads were aligned on scaffolds larger than 500 bp with bowtie2 software and scaffold […]


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PhyloPythia in publications

 (37)
PMCID: 5840735
PMID: 29556373
DOI: 10.1186/s12263-018-0594-6

[…] the taxonomy determination is to compare the k-mer profiles of the metagenomics contigs with k-mer profiles obtained from a reference database. this has been implemented in tools like kraken [] or phylopythia [] (for a review of programs, see []),, to understand the underlying causes of a community change and potential effect, functional profiling needs to be performed (fig. ). this part […]

PMCID: 5606693
PMID: 28781346
DOI: 10.1264/jsme2.ME17022

[…] of sequence data was obtained from this m82 culture using the illumina hiseq platforms, yielding a 208-mbp metagenome containing 144,759 scaffolds between 200 and 482,817 bp (n50 size=4,619 bp, ). phylopythia assigned approximately 55% of the sequence fragments to the phylum proteobacteria (), and binning of these scaffolds into population genomes was facilitated by plotting coverage […]

PMCID: 5462947
PMID: 28642744
DOI: 10.3389/fmicb.2017.01023

[…] a variety of different k-mer lengths, a minimum k-mer length of 33 and a maximum k-mer length of 73 were applied with 10-mer iterations. contigs greater than 1000 bp were taxonomically binned using phylopythia s+ (gregor et al., ). this involved the analysis of marker genes and k-mer profiles. the coverage of individual contigs was calculated using bbmap (v. 35.02) […]

PMCID: 5356057
PMID: 28302780
DOI: 10.1128/genomeA.00033-17

[…] version 8.5.1 (http://www.clcbio.com/products/clc-genomics-workbench) and spades version 3.5.1 (). assembled contigs were grouped into genome bins with vizbin () and taxonomy assessed with phylopythia (). metagenomic reads were mapped against binned contigs and reassembled using spades., the final draft genome contained 128 contigs of 5000 bp to 243,670 bp in length and an n50 […]

PMCID: 5389567
PMID: 28206648
DOI: 10.1093/nar/gkx082

[…] and machine learning (,,), svms have been the tool of choice for many multi-class classification problems (,,). for our multi-cancer classification, we followed an svm-based approach analogous to phylopythia (,), our classifier of metagenomes., we ran a monte-carlo cross-validation approach for 1 000 iterations. in each iteration, we trained the svm classifier using a random sample comprising […]


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PhyloPythia institution(s)
Bioinformatics and Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
PhyloPythia funding source(s)
Supported by the US Department of Energy’s Office of Science, Biological and Environmental Research Program, the University of California, Lawrence Livermore National Laboratory, under contract W-7405-Eng-48; Lawrence Berkeley National Laboratory under contract DE-AC03-76SF00098, and Los Alamos National Laboratory under contract W-7405-ENG-36.

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