Main Page

From Bioinformatics Software
Revision as of 01:31, 18 November 2009 by Beiko (talk | contribs)
Jump to navigationJump to search
Using GenGIS to investigate the distribution of photorhodopsin genes around the Galapagos Islands (data courtesy of <Rob... who did we get this data from - Adrian?>).

Welcome to the Bioinformatics Software and Resources page.

<-- Can someone come up with a logo?

<-- Cool molecule icon added by Mr. Parks


Key: P = phylogenetics, S = statistics, B = biogeography, V = visualization, G = genomics, M = metagenomics, L = lateral genetic transfer

  • GenGIS: an application that allows users to combine digital map data with information about biological sequences collected from the environment. GenGIS provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries. (PSBVM)
  • Radié: a tool that allows characters to be visualized against the background of a phylogenetic tree. The software includes several different visual and numeric representations of the ‘convexity’ of a given character, in other words the extent to which different character traits form distinct groups within the tree. (PV)
  • STAMP: (SMV)
  • EvolSimulator: A simulation test bed for hypotheses of genome evolution. (PL)
  • EEEP (Efficient Evaluation of Edit Paths): software to infer putative pathways of lateral genetic transfer by comparing gene trees against a rooted reference tree (PL)
  • VAREB?
  • WOOF?
  • GANN?

Web Services


  • Links to STAMP datasets?
  • Datasets used in GenGIS (Parks et al., Genome Research 2009)
  • Simulated data for 'The impact of reticulate evolution on genome phylogeny' (Beiko et al., Systematic Biology 2008)
  • LGT in 144 genomes