PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change.
PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change.
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DOI：
10.1186/1471-2148-6-1
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发表时间：
2006-01-03
影响因子：
3.4
通讯作者：
Gibbs MJ
中科院分区：
文献类型：
--
作者：
Fourment M;Gibbs MJ
系统发育通常用于分析基因、基因组和物种之间的差异。从树的分支长度计算的父距离描述了树所代表的遗传变化的量，并且通常与其他突变的测量进行比较，以调查替代过程或树与原始数据的拟合优度。到目前为止，还没有通用的工具来计算教父距离，并将它们与其他遗传距离测量相关联。PATRISTICv1.0是一个Java程序，可以计算一系列文件格式的大树的教父距离，并允许对其他程序计算的距离矩阵进行图形和统计解释。该软件克服了分析序列信号的一些逻辑障碍。除了计算教父距离外，它还提供任何矩阵组合的图，计算常用的统计数据，允许输入隔离日期等数据，并使用匹配的物种或基因标签重新排序矩阵。它将被用来分析病毒的突变率、取代饱和度和进化。它可以在上获得，并且需要Java运行时环境。
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 and requires the Java runtime environment.
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DOI：
10.1073/pnas.0501589102
发表时间：
2005-04-19
影响因子：
11.1
作者：
Grus, WE;Shi, P;Zhang, JZ
通讯作者：
Zhang, JZ
影响因子：
56.9
作者：
Korber, B;Muldoon, M;Bhattacharya, T
通讯作者：
Bhattacharya, T
影响因子：
3.4
作者：
Fourment M;Gibbs MJ
通讯作者：
Gibbs MJ
影响因子：
2.4
作者：
Hayward, DC;Bastiani, MJ;Ball, EE
通讯作者：
Ball, EE
影响因子：
9.8
作者：
Holmes EC;Ghedin E;Miller N;Taylor J;Bao Y;St George K;Grenfell BT;Salzberg SL;Fraser CM;Lipman DJ;Taubenberger JK
通讯作者：
Taubenberger JK