FASconCAT: Convenient handling of data matrices

被引：417

作者：

Kueck, Patrick ^{[1
]}

Meusemann, Karen ^{[1
]}

机构：

[1] Zool Forsch Museum Alexander Koenig, Mol Bioinformat Unit, D-53113 Bonn, Germany

来源：

MOLECULAR PHYLOGENETICS AND EVOLUTION | 2010年 / 56卷 / 03期

关键词：

Concatenation; Software; Sequence data; Structure data; Perl; PHYLOGENETIC ANALYSES; MIXED MODELS; DIVERSIFICATION; ANTS;

D O I：

10.1016/j.ympev.2010.04.024

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

FASconCAT is a user-friendly software that concatenates rapidly different kinds of sequence data into one supermatrix file. Output files are either in FASTA, PHYLIP or NEXUS format and are directly loadable in phylogenetic programs like PAUP*, RAxML or MrBayes. FASconCAT can handle FASTA, PHYLIP and CLUSTAL formatted input files in one single run. It provides useful information about each input file and the concatenated supermatrix. For example, the program provides the range information of each concatenated gene (partition) and delivers a check list of all concatenated sequences (taxa). Information about the base composition of single input files and the resulting supermatrix is supplied for nucleotide data. For given structure strings (e.g. secondary structures) it displays single unpaired (loop) and paired (stem) positions after the concatenation process. Optionally, FASconCAT generates NEXUS files of concatenated sequences, either with MrBayes commands directly executable in PAUP* and MrBayes, or without any specific commands. If favoured, FASconCAT dispenses output files in PHYLIP format with relaxed (unlimited signs) or restricted taxon names (up to ten signs) while sequences are printed in non-interleaved format. FASconCAT is implemented in Perl and freely available from http://software.zfmk.de. It runs on UNIX and MS Windows operating systems. (C) 2010 Elsevier Inc. All rights reserved.

引用

页码：1115 / 1118

页数：4

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