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PhyloWGS specifications

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Unique identifier OMICS_07695
Name PhyloWGS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Quaid Morris <>

Publication for PhyloWGS

PhyloWGS in publications

 (11)
PMCID: 5717219
PMID: 29208983
DOI: 10.1038/s41598-017-16813-4

[…] estimation of the prevalence of a given clone can be inaccurate, and the corresponding heterogeneity results may be misleading. existing methods that capture snvs and cnas in the same model (i.e., phylowgs, spruce and canopy) require running a cna-calling algorithm before heterogeneity analysis, but accurate cna characterization also depends on heterogeneity analysis.table 1 , most existing […]

PMCID: 5723949
PMID: 29279850
DOI: 10.1155/2017/5482750

[…] of cells harboring each event. some tumor progression analysis tools combine vafs of snvs and population frequencies of structure variations to reconstruct subclonal composition and tumor evolution. phylowgs [] uses copy number alterations to correct the vafs of affected snvs and greatly improves subclonal reconstruction compared to existing methods. as tumor is a heterogeneity system, jiang et […]

PMCID: 5656607
PMID: 29070816
DOI: 10.1038/s41467-017-01062-w

[…] found to be non-aberrant by absolute (scnas were absent and thus could not be used to determine optimal solutions during the manual curation step of absolute) were excluded from analysis., we used phylowgs to reconstruct complete genotypes and phylogenetic relationships of tumor subpopulations from ccf values of ssnvs, indels, and scnas. phylowgs is capable of performing on both wes as well […]

PMCID: 5647443
PMID: 29044127
DOI: 10.1038/s41598-017-13338-8

[…] a more realistic model than synthetic data to assess the performance of different computational methods. in this work we present a comparison of the performance of pyclone, clomial, sciclone, and phylowgs (algorithms in bold in tableĀ ) on our ground truth datasets. we selected these four algorithms because they can be applied directly and simultaneously to all of our deep-targeted data […]

PMCID: 5469877
PMID: 28659971
DOI: 10.3389/fgene.2017.00083

[…] and uses a dirichlet process prior over phylogenetic trees to group snvs into clones. it employs bayesian inference, based on mcmc sampling, to infer a distribution over possible evolutionary trees. phylowgs (deshwar et al., ) builds on phylosub and allows the reconstruction of tumor evolution from snvs and cnas obtained from whole genome sequencing data. citup (malikic et al., ) proposes […]

PhyloWGS institution(s)
Edward S Rogers Sr Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada

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