PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting clade-defining polymorphism. This functionality has been implemented using the tabix tool on the server side, providing simple and rapid access to the information at each tree node, including informative SNPs stored in VCF-similar files. These informative variants have been established by comparing allele frequencies between strain-types using ancestral node comparisons and FST measures of population differentiation.

Features

  • Phylogeny representation of samples
  • Genome browser
  • Map distribution of alleles and spoligotypes
  • Sample analysis and positioning in the tree

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Categories

Bio-Informatics

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Additional Project Details

Operating Systems

Linux

Intended Audience

Science/Research

Programming Language

Python, Perl, PHP, JavaScript

Database Environment

Other file-based DBMS

Related Categories

Python Bio-Informatics Software, Perl Bio-Informatics Software, PHP Bio-Informatics Software, JavaScript Bio-Informatics Software

Registered

2014-09-22