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PhyloSub specifications

Information


Unique identifier OMICS_05980
Name PhyloSub
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 PhyloSub

PhyloSub in publications

 (9)
PMCID: 5723949
PMID: 29279850
DOI: 10.1155/2017/5482750

[…] two hypotheses to limit the number of possible trees, which can handle up to 25 snvs. detection of clones based on snv frequency data is necessary for inferring phylogeny. jiao et al. [] proposes phylosub, a bayesian nonparametric model, to infer the phylogeny and genotype of the major subclonal lineages represented in the population of cancer cells. miller et al. [] proposed a variational […]

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

[…] regions cannot be assigned to any cluster., deshwar and colleagues propose phylowgs, a non-parametric bayesian method to cluster snvs and infer tumour phylogenetic trees. unlike his predecessor phylosub, phylowgs introduces a phylogenic correction for vafs in loci in regions with copy number alterations. phylowgs employs an mcmc method for inference. this method can be applied to a single […]

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

[…] tumor sample. it first groups together mutations with similar frequencies, and then uses an iterative procedure to build evolutionary paths for such groups, starting from simple (height 1) trees. phylosub (jiao et al., ) considers vafs from deep sequencing experiments to infer the evolutionary relationship of clones, and uses a dirichlet process prior over phylogenetic trees to group snvs […]

PMCID: 5813714
PMID: 28193548
DOI: 10.1016/j.bbcan.2017.02.001

[…] 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 status and population frequencies are required […]

PMCID: 5269563
PMID: 27998038
DOI: 10.1002/cam4.953

[…] significantly enriched pathway was considered if the adjusted p < 0.1., the evolutionary history of each of the 23 tumors was constructed on the basis of the somatic mutations’ reads count using phylosub . this approach made use of bayesian inference and markov chain monte carlo sampling (with 2500 samplings) to estimate the number of clonal lineages and their ancestry. we only considered […]


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PhyloSub institution(s)
Department of Molecular Genetics, University of Toronto, Toronto, Canada

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