articleCladisticsJul 7, 2010BRONZE OA

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

GVGaurav VaidyaDJDavid J. LohmanRMRudolf Meier

National University of Singapore

PubMed
Indexed incrossrefpubmed

Abstract

We present SequenceMatrix, software that is designed to facilitate the assembly and analysis of multi-gene datasets. Genes are concatenated by dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into the program window. A multi-gene dataset is concatenated and displayed in a spreadsheet; each sequence is represented by a cell that provides information on sequence length, number of indels, the number of ambiguous bases ("Ns"), and the availability of codon information. Alternatively, GenBank numbers for the sequences can be displayed and exported. Matrices with hundreds of genes and taxa can be concatenated within minutes and exported in TNT, NEXUS, or PHYLIP formats, preserving both…

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Topics & keywords

Topics
Keywords
  • GenBank
  • ASCII
  • Software
  • Gene
  • Computer science
  • Set (abstract data type)
  • Biology
  • Mega-
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