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

Mathieu Fourment,Mark J Gibbs

doi:10.1186/1471-2148-6-1

Abstract

BackgroundPhylogenies 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.ResultsPATRISTICv1.0 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.ConclusionThe 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 and requires the Java runtime environment.

Highlights

Phylogenies are commonly used to analyse the differences between genes, genomes and species
Maximum likelihood (ML) methods provide the best estimates of evolutionary change and genetic difference by modelling substitutions
Models are used to calculate branch-lengths that take into account the superimposition of substitutions and the similarities between one sequence or taxon and all others represented in the dataset [13]

Summary

Conclusion

A phylogenetic tree usually represents signals drawn from many sites in the sequences from which it was inferred, and it represents a hierarchy of those signals that may be nested. The relationships between phylogenetic trees and sequences of interest are often complex and obscure. Comparisons of patristic distances and other measures of genetic change allow the relationships to be analysed. PATRISTICv1.0 was developed to permit expedient comparisons and analyses. The program reads trees and distance matrices produced by the most commonly used software without editing. Re-formatting is a time consuming element of multiple sequence and phylogenetic analysis and for that reason PATRISTICv1.0 creates no new intermediate formats. The program is likely to be used to analyse recombination, rates of mutation and substitutional saturation and the evolution of rapidly evolving entities such as viruses

Background

Results and Discussion