phyC specifications

Information


Unique identifier OMICS_12695
Name phyC
Alternative name Phylogenetic tree Clustering
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Variant allele frequency, Edge matrix and edge length vector from reconstructed sub-clonal evolutionary trees
Output data Cluster assignments, Multidimensional scaling configuration of trees in clusters, Sub-clonal diversity of trees in clusters
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.2.0
Stability Stable
Requirements Ape, igraph, ggplot2, grDevices, png, RColorBrewer
Source code URL https://codeload.github.com/ymatts/phyC/zip/master
Maintained Yes

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Documentation


Maintainer


  • person_outline Yusuke Matsui <>

phyC article

phyC citation

2011
PMCID: 3087796

[…] each microsatellite allele between the two samples 1976 and 2003 using powermarker [33]. the distribution obtained is referred to as the empirical distribution. the differentiation obtained for the phyc locus was ranked in this distribution. this rank gave an empirical p-value. to assess if the high mutation rate observed at the microsatellite loci [34] might impair this test, we performed […]

phyC institution(s)
Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan; Division of Health Medical Computational Science, Health Intelligence Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan; Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

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