PhyloSub statistics

info info

Citations per year

info

Tool usage distribution map

info info

Associated diseases

info

Popular tool citations

chevron_left Tumor purity and heterogeneity estimation chevron_right
Want to access the full stats & trends on this tool?

Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Quaid Morris

Publication for PhyloSub

PhyloSub citations

 (9)
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

[…] the 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 Bay […]

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

[…] diploid 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 sa […]

library_books

Computational Methods for Characterizing Cancer Mutational Heterogeneity

2017
Front Genet
PMCID: 5469877
PMID: 28659971
DOI: 10.3389/fgene.2017.00083

[…] gle 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 into […]

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

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

library_books

Whole‐exome sequencing predicted cancer epitope trees of 23 early cervical cancers in Chinese women

2016
PMCID: 5269563
PMID: 27998038
DOI: 10.1002/cam4.953

[…] 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 tre […]

call_split

Longitudinal copy number, whole exome and targeted deep sequencing of 'good risk' IGHV mutated CLL patients with progressive disease

2016
Leukemia
PMCID: 4861248
PMID: 26847028
DOI: 10.1038/leu.2016.10
call_split See protocol

[…] lusters remain the same over time. (2) Expanding: all mutations in a cluster increase over time. (3) Evolving: new mutations in later samples or one or more mutations in a cluster increase over time. Phylosub was used for tumour phylogeny analysis to predict the most likely order of mutation events and classify either linear or branching evolution patterns. PAX5 enhancer region was screened as des […]


Want to access the full list of citations?
PhyloSub institution(s)
Department of Molecular Genetics, University of Toronto, Toronto, Canada

PhyloSub reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PhyloSub