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Using GenGIS to investigate the distribution of photorhodopsin genes around the Galapagos Islands (data courtesy of Adrian Sharma, Jeremy Koenig, and Olga Zhaxybayeva).

Welcome to the Bioinformatics Software and Resources page.

Software

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

  • EvolSimulator: a simulation test bed for hypotheses of genome evolution. (PL)
  • GANN: a machine learning method designed with the complexities of transcriptional regulation in mind.
  • 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)
  • PICA: genotype-phenotype data mining software (G).
  • 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)
  • RITA: Rapid Identification of Taxonomic Assignments for metagenomic fragments (M).
  • rSPR: software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests. (PL)
  • SPRSupertrees: software to calculate rooted supertrees that minimize the SPR distance. (PL)
  • STAMP: a software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. (SMV)
  • VAREB [to be added]
  • WOOF: a tool designed to rigourously apply the principle of visual alignment validation. (SA)

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Datasets

Contributors