PhyloWGS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PhyloWGS
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Tool usage distribution map

This map represents all the scientific publications referring to PhyloWGS per scientific context
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Associated diseases

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Popular tool citations

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Protocols

PhyloWGS specifications

Information


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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Documentation


Maintainer


  • person_outline Quaid Morris

Publication for PhyloWGS

PhyloWGS citations

 (11)
call_split

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies

2017
Sci Rep
PMCID: 5717219
PMID: 29208983
DOI: 10.1038/s41598-017-16813-4
call_split See protocol

[…] Unlike previous methods such as phyloWGS, SPRUCE and Canopy, which capture CNA or SNV events as the entities in the model, our model THEMIS and its predecessor TITAN directly model individual genomic positions as the entities in the […]

library_books

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees

2017
Biomed Res Int
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 a […]

library_books

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

2017
Nat Commun
PMCID: 5656607
PMID: 29070816
DOI: 10.1038/s41467-017-01062-w

[…] ples 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 as […]

library_books

Engineered in vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer

2017
Sci Rep
PMCID: 5647443
PMID: 29044127
DOI: 10.1038/s41598-017-13338-8

[…] PyClone 0.13.0 available from http://compbio.bccrc.ca/software/pyclone.Clomial 1.3.0 available at R-bioconductor.SciClone available from https://github.com/genome/sciclone.PhyloWGS available from https://github.com/morrislab/phylowgs. […]

library_books

Computational Methods for Characterizing Cancer Mutational Heterogeneity

2017
Front Genet
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 a combi […]

library_books

Advances in understanding tumour evolution through single cell sequencing*

2017
Biochim Biophys Acta
PMCID: 5813714
PMID: 28193548
DOI: 10.1016/j.bbcan.2017.02.001

[…] ence is then a two-step process: It first uses a hypothesis testing framework to establish subclones and their pairwise relationships and then applies a genetic algorithm to find a matching phylogeny.PhyloWGS  extends the probabilistic framework of PhyloSub  to integrate copy number information. It is also the first approach to model overlaps between CNA and SNV data. Estimates of CNA copy number […]


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

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