Difference between revisions of "Main Page"

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* [[NetworkDiversity| Network Diversity]]: calculation of beta diversity over phylogenetic networks. (P)
 
* [[NetworkDiversity| Network Diversity]]: calculation of beta diversity over phylogenetic networks. (P)
 
* [[PICA]]: genotype-phenotype data mining software (G).
 
  
 
* [[RITA]]: Rapid Identification of Taxonomic Assignments for metagenomic fragments (M).
 
* [[RITA]]: Rapid Identification of Taxonomic Assignments for metagenomic fragments (M).
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* [[STAMP]]: a software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. (SMV)
 
* [[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]
 
  
 
== Older Software ==
 
== Older Software ==
 +
 +
The following software packages have largely been superseded by others in the above list, or by software written by others. The software should still work, but we can no longer offer significant support for it.
  
 
* [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)
 +
 +
* [[PICA]]: genotype-phenotype data mining software (G).
  
 
* [http://kiwi.cs.dal.ca/~beiko/software-and-data/radie 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)
 
* [http://kiwi.cs.dal.ca/~beiko/software-and-data/radie 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)
  
* [http://bioinformatics.org.au/gann/ GANN]: a machine learning method designed with the complexities of transcriptional regulation  
+
* [http://bioinformatics.org.au/gann/ GANN]: a machine learning method designed with the complexities of transcriptional regulation in mind.
in mind.
+
  
 
* [http://bioinformatics.org.au/woof/ WOOF]: a tool designed to rigourously apply the principle of visual alignment validation. (SA)
 
* [http://bioinformatics.org.au/woof/ WOOF]: a tool designed to rigourously apply the principle of visual alignment validation. (SA)
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* [http://ratite.cs.dal.ca/SeqMonitor SeqMonitor]
 
* [http://ratite.cs.dal.ca/SeqMonitor SeqMonitor]
 
* [http://bio.mquter.qut.edu.au/Moa/ MOAMap]
 
* [http://bio.mquter.qut.edu.au/Moa/ MOAMap]
* MOA (to be added)
 
* Visual MOA (to be added)
 
 
* [http://fester.cs.dal.ca/manuel MANUEL]
 
* [http://fester.cs.dal.ca/manuel MANUEL]
  

Revision as of 00:57, 18 June 2012

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 (Currently Supported)

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)
  • 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)
  • 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)

Older Software

The following software packages have largely been superseded by others in the above list, or by software written by others. The software should still work, but we can no longer offer significant support for it.

  • 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)
  • GANN: a machine learning method designed with the complexities of transcriptional regulation in mind.
  • WOOF: a tool designed to rigourously apply the principle of visual alignment validation. (SA)

Web Services

Mailing list

  • Join our mailing list to keep informed about new developments.

Datasets

Contributors