Fourment Mathieu, Gibbs Mark J
School of Botany and Zoology, The Australian National University, Canberra ACT 0200, Australia.
BMC Evol Biol. 2006 Jan 3;6:1. doi: 10.1186/1471-2148-6-1.
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.
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.
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.
系统发育树常用于分析基因、基因组和物种之间的差异。根据树分支长度计算的祖先距离描述了一棵树所代表的遗传变化量，并且通常与其他突变度量进行比较，以研究替代过程或树与原始数据的拟合优度。到目前为止，还没有通用的工具可用于计算祖先距离并将其与其他遗传距离度量相关联。
PATRISTICv1.0是一个Java程序，它可以从多种文件格式的大树中计算祖先距离，并允许对其他程序计算的距离矩阵进行图形化和统计解释。
该软件克服了分析序列信号的一些逻辑障碍。除了计算祖先距离外，它还为矩阵的任何组合提供图表，计算常用统计量，允许输入隔离日期等数据，并使用匹配的物种或基因标签对矩阵进行重新排序。它将用于分析突变率和替代饱和度以及病毒的进化。可在http://biojanus.anu.edu.au/programs/上获取，并且需要Java运行时环境。
