Difference between revisions of "Main Page"
From Bioinformatics Software
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== Software == | == Software == | ||
| − | Key: P = phylogenetics, S = statistics, B = biogeography, V = visualization, G = genomics, M = metagenomics, L = lateral genetic transfer | + | Key: P = phylogenetics, S = statistics, B = biogeography, V = visualization, G = genomics, M = metagenomics, L = lateral genetic transfer, A = sequence alignment |
| Line 19: | Line 19: | ||
* [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. ( | + | * [http://bioinformatics.org.au/woof/ WOOF]: a tool designed to rigourously apply the principle of visual alignment validation. (SA) |
| + | |||
| + | * [http://bioinformatics.org.au/gann/ GANN]: a machine learning method designed with the complexities of transcriptional regulation in mind. | ||
* VAREB? | * VAREB? | ||
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== 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)
- 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)
- 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
- SeqMontior
- MOA (to be added)
- Visual MOA (to be added)
- MANUEL
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
