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Welcome to the Bioinformatics Web of Wisdom.
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__NOTOC__
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[[Image:GenGIS_galapagos.jpg|frame|right|Using GenGIS to investigate the distribution of photorhodopsin genes around the Galapagos Islands (data courtesy of Adrian Sharma, Jeremy Koenig, and Olga Zhaxybayeva).]]
  
<-- '''Can someone come up with a logo?'''
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Welcome to the Bioinformatics Software and Resources page.
  
== Purpose ==
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== Software (Currently Supported) ==
This wiki is meant to be a collective notepad for the bioinformatics folks from the Beiko/Blouin/Zeh/Keselj lab. The structure has yet to be defined but I propose a few entries such as
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Key: P = phylogenetics, S = statistics, B = biogeography, V = visualization, G = genomics, M = metagenomics, L = lateral genetic transfer, A = sequence alignment
* [[Schedule]]
 
* [[Useful Software]]
 
* [[open problems]] and cool ideas,  
 
* [[:Category:howto | HOWTO]]
 
* [[Literature]]
 
* [[Articles submitted or in press]]
 
* [[Resources]]
 
  
== Projects Page ==
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* [[simDEF | simDEF]]: Definition-based Semantic Similarity Measure of GO Terms for Functional Similarity Analysis of Genes.
* [[Influenza A]]
 
  
== Servers and Services ==
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* [[ExpressBetaDiversity | Express Beta Diversity (EBD)]]: taxon- and phylogenetic-based beta diversity measures. (P)
In Alphabetical order
 
* [http://www.ace-net.ca ace-net]
 
* [[moa]] - Coming one of these aeons!
 
* [[kiwi]]
 
* [[morticia]]
 
* [[pepito]]
 
* [[vibrio]]
 
  
== Groups ==
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* [[FCP | Fragment classification package (FCP)]]: Homology- and composition-based classifiers for assigning a taxonomic attribution to metagenomic fragments. (GML)
* [http://www.cs.dal.ca/~beiko/ Beiko]
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* [http://www.cs.dal.ca/~cblouin Blouin]
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* [http://kiwi.cs.dal.ca/GenGIS 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)
* [http://www.cs.dal.ca/~vlado Keselj]
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* [http://www.cs.dal.ca/~nzeh Zeh]
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* [[NetworkDiversity| Network Diversity]]: calculation of beta diversity over phylogenetic networks. (P)
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* [http://kiwi.cs.dal.ca/Software/rSPR rSPR]: software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests. (PL)
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* [[SPANNER]]: Homology-based taxonomic classification of protein sequences. (GML)
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* [[SPRSupertrees]]: software to calculate rooted supertrees that minimize the SPR distance. (PL)
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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)
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* PICA: genotype-phenotype data mining software (G). A [https://github.com/univieCUBE/PICA new version] of the software has been developed by the [http://cube.univie.ac.at/people Rattei group] at Universität Wien and is hosted on Github . The older version from our lab, which is no longer supported, can be found [[PICA | here]].
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== Older Software ==
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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.
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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)
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* [http://bioinformatics.org.au/evolsim/ EvolSimulator]: a simulation test bed for hypotheses of genome evolution. (PL)
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* [[RITA]]: Rapid Identification of Taxonomic Assignments for metagenomic fragments (M).
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* [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)
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* [http://bioinformatics.org.au/gann/ GANN]: a machine learning method designed with the complexities of transcriptional regulation in mind.
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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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== Mailing list ==
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* Join our [http://ratite.cs.dal.ca/software_email_list/subscribe mailing list] to keep informed about new developments.
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== Datasets ==
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* [http://kiwi.cs.dal.ca/GenGIS/Datasets Datasets used in GenGIS] (Parks et al., Genome Research 2009)
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* [http://kiwi.cs.dal.ca/Software/STAMP_example_datasets STAMP datasets]
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* [http://bioinformatics.org.au/lgt144/ Lateral genetic transfer in 144 genomes dataset] (Beiko et al., Proc. Natl. Acad. Sci. 2005)
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* Simulated data for 'The impact of reticulate evolution on genome phylogeny' (Beiko et al., Systematic Biology 2008) [to be added]
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== Contributors ==
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* [http://kiwi.cs.dal.ca/~beiko/ Robert Beiko]
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* [http://www.cs.dal.ca/~cblouin Christian Blouin]
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* [http://dparks.wikidot.com/ Donovan Parks]
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* [http://www.cs.dal.ca/~whidden Chris Whidden]
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* Norman MacDonald
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* [[TBD]]
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* [[MEGASAT]]

Latest revision as of 20:51, 4 September 2015

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

  • simDEF: Definition-based Semantic Similarity Measure of GO Terms for Functional Similarity Analysis of Genes.
  • 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)
  • rSPR: software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests. (PL)
  • SPANNER: Homology-based taxonomic classification of protein sequences. (GML)
  • 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)
  • PICA: genotype-phenotype data mining software (G). A new version of the software has been developed by the Rattei group at Universität Wien and is hosted on Github . The older version from our lab, which is no longer supported, can be found here.

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.

  • EvolSimulator: a simulation test bed for hypotheses of genome evolution. (PL)
  • RITA: Rapid Identification of Taxonomic Assignments for metagenomic fragments (M).
  • 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)

Mailing list

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

Datasets

Contributors