Gist began as a project to develop a sequence classifier based on arbitrary input classes, and has developed into a high-precision, noise-tolerant taxonomic classifier focused specifically on the problem of annotating short (76 nt and higher), unassembled reads with little or no quality filtering
TreeMaker is a software that allows the interactive building and editing of a taxonomy and its conversion into a phylogeny for the above calculations. It also allows the editing of site abundance and species richness data. This data may be imported from and exported to a variety of formats for interoperability with other programs. While it is mainly intended for use in conservation and biodiversity, it can be used as a simple tool for building phylogenies.
TaxMan (Taxonomy database Manager) is a software package that uses freely available bioinformatics tools to allow rapid assembly, storage and analysis of large aligned DNA and protein sequence datasets for user-defined sets of species and genes. Sequence data are obtained from GenBank format files on the basis of annotation and / or sequence similarity. Consensus sequences are built and aligned automatically, and aligned sequences are stored in a database. By using the stored aligned sequences, large concatenated protein and DNA multiple sequence alignments can be rapidly generated for subsets of the dataset. Trees resulting from phylogenetic analysis can also be stored, and compared with a reference taxonomy.
The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh