PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change

BMC Evol Biol. 2006 Jan 3;6:1. doi: 10.1186/1471-2148-6-1.

Abstract

Background: Phylogenies are commonly used to analyse the differences between genes, genomes and species. Patristic distances calculated from tree branch lengths describe the amount of genetic change represented by a tree and are commonly compared with other measures of mutation to investigate the substitutional processes or the goodness of fit of a tree to the raw data. Up until now no universal tool has been available for calculating patristic distances and correlating them with other genetic distance measures.

Results: PATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs.

Conclusion: The software overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses. It is available at http://biojanus.anu.edu.au/programs/ and requires the Java runtime environment.

Publication types

  • Comparative Study

MeSH terms

  • Decision Trees
  • Evolution, Molecular*
  • Genetic Variation
  • Internet
  • Likelihood Functions
  • Mutation*
  • Phylogeny*
  • Software*