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Tools and Databases

Tool Development for Evolutionary Analyses of Genomes

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  • REFGEN an online sequence manager for easy control of database sequences enabling renaming of long sequence labels prior to phylogenetic analyses which almost always requires short sequence names
  • TREENAMER an online tree label manger that will illustrate tree labels given the REFGEN output file. Phylogenetic trees for publication almost always require species names and/or database accession numbers; this program enables the user to manage this information.
  • easyRAx a simple script that wraps around the command line program RAxML. RAxML is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. RAxML is available here.
  • Species Autocorrect: 839 taxa sampled from NCBI, DOE JGI and BROAD compiled into a MS Word AutoCorrect file in order to 'automagically' italicise taxon names.
  • FDF BLAST (link - coming soon)

Gene and Genome databases

  • Hyphochytrium EST database (link - coming soon)
  • Heteromita Genome Sequence Survey database (link - coming soon)
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