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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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Maintainer
- person_outline Quaid Morris
Publication for PhyloWGS
PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.
PhyloWGS citations
(11)Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies
[…] 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 […]
An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees
[…] 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 […]
Resistance to checkpoint blockade therapy through inactivation of antigen presentation
[…] 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 […]
Engineered in vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer
[…] 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. […]
Computational Methods for Characterizing Cancer Mutational Heterogeneity
[…] 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 […]
Advances in understanding tumour evolution through single cell sequencing*
[…] 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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