Difference between revisions of "Main Page"

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Welcome to the Bioinformatics Software and Resources page.
 
Welcome to the Bioinformatics Software and Resources page.
 
  
 
== Software ==
 
== Software ==
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* VAREB?
 
* VAREB?
 
  
 
== Web Services ==
 
== Web Services ==
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* Simulated data for 'The impact of reticulate evolution on genome phylogeny' (Beiko et al., Systematic Biology 2008)
 
* Simulated data for 'The impact of reticulate evolution on genome phylogeny' (Beiko et al., Systematic Biology 2008)
 
* LGT in 144 genomes
 
* LGT in 144 genomes
 
  
 
== Contributors ==
 
== Contributors ==

Revision as of 20:42, 22 November 2009

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.

Software

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


  • 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: a software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. (SMV)
  • EvolSimulator: a simulation test bed for hypotheses of genome evolution. (PL)
  • WOOF: a tool designed to rigourously apply the principle of visual alignment validation. (SA)
  • GANN: a machine learning method designed with the complexities of transcriptional regulation in mind.
  • VAREB?

Web Services

Datasets

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

Contributors