MulRF: a software package for phylogenetic analysis using multi-copy gene trees

被引：19

作者：

Chaudhary, Ruchi ^{[1
]}

Fernandez-Baca, David ^{[2
]}

Burleigh, John Gordon ^{[1
]}

机构：

[1] Univ Florida, Dept Biol, Gainesville, FL 32611 USA

[2] Iowa State Univ, Dept Comp Sci, Ames, IA 50011 USA

来源：

BIOINFORMATICS | 2015年 / 31卷 / 03期

基金：

美国国家科学基金会;

关键词：

SPECIES TREES; MAXIMUM-LIKELIHOOD; ALGORITHMS;

D O I：

10.1093/bioinformatics/btu648

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

MulRF is a platform-independent software package for phylogenetic analysis using multi-copy gene trees. It seeks the species tree that minimizes the Robinson-Foulds (RF) distance to the input trees using a generalization of the RF distance to multi-labeled trees. The underlying generic tree distance measure and fast running time make MulRF useful for inferring phylogenies from large collections of gene trees, in which multiple evolutionary processes as well as phylogenetic error may contribute to gene tree discord. MulRF implements several features for customizing the species tree search and assessing the results, and it provides a user-friendly graphical user interface (GUI) with tree visualization. The species tree search is implemented in C++ and the GUI in Java Swing.

引用

页码：432 / 433

页数：2

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