TaxonDNA: Extensible Bioinformatics in Java

Welcome to TaxonDNA!

TaxonDNA is a collection of tools for manipulating datasets with multiple species. The following tools are currently available are:

• Species Identifier provides a set of tools for exploring intra- and interspecific genetic distances, matching sequences, and clustering sequences based on pairwise distances. It helps determine whether two sequences are likely conspecific based on pairwise distances, and can calculate pairwise distances for large datasets. It was designed to provide the analyses presented in Meier et al, 2006 (Best match, Best close match and All Species Barcodes).

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• Sequence Matrix facilitates the assembly of phylogenetic data matrices with multiple genes. Files for individual genes are dragged and dropped into a window and the sequences are concatenated. A table provides an overview over how much sequence information is available for the different genes and species. The user can request Sequence Matrix generate a wide variety of character and taxon sets (e.g. a taxon set with all species that have more than a specified number of genes or basepairs). The concatenated sequences can be exported in NEXUS or TNT format. Individual sequences can be excluded from being exported.

  This software was presented at Hennig 2009 and published as Vaidya et al, 2010.

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References

• Meier, R., Kwong, S., Vaidya, G., Ng, Peter K. L. (2006) DNA Barcoding and Taxonomy in Diptera: a Tale of High Intraspecific Variability and Low Identification Success. Systematic Biology, 55: 715-728.
• Vaidya, G., Lohman, D. J., Meier, R. (2010) SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics, early view.