Difference between revisions of "Main Page"

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== Software ==
 
== Software ==
Key: P = phylogenetics, S = statistics, B = biogeography, V = visualization, G = genomics, M = metagenomics, L = lateral genetic transfer
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Key: P = phylogenetics, S = statistics, B = biogeography, V = visualization, G = genomics, M = metagenomics, L = lateral genetic transfer, A = sequence alignment
  
  
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* [http://bioinformatics.org.au/eeep/ 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)
 
* [http://bioinformatics.org.au/eeep/ 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)
  
* [http://bioinformatics.org.au/woof/ WOOF]: a tool designed to rigourously apply the principle of visual alignment validation. (S)
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* [http://bioinformatics.org.au/woof/ WOOF]: a tool designed to rigourously apply the principle of visual alignment validation. (SA)
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* [http://bioinformatics.org.au/gann/ GANN]: a machine learning method designed with the complexities of transcriptional regulation in mind.
  
 
* VAREB?
 
* VAREB?
 
* GANN?
 
  
 
== Web Services ==
 
== Web Services ==

Revision as of 15:07, 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