Tools

A list of bioinformatics related tools available through our website…
Some of these tools will leave this website and take you to ‘github’, a website for hosting programming projects. All are open-source and you are free to modify, make suggestions or change, as long as you cite their relevant paper or website address/authors.

Both REFGEN and TREENAMER are hosted on this server but will open in a new page.

  • 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. You will need to check out the source.
  • Taxa Autocorrect – a tool to ‘automagically’ italicise taxon names, compiled from 839 taxa sampled from NCBI, DOE JGI and BROAD. Currently MS Word only
  • fdfBLAST – find differential fusion BLAST, a tool to look for differentially distributed gene fusions within a group of proteomes