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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

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)

• PICA: genotype-phenotype data mining software (G).

• rSPR: software to calculate rooted subtree-prune-and-regraft distances and rooted agreement forests. (PL)

• STAMP: a software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. (SMV)

• 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)

• 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 [to be added]

Web Services

• SeqMonitor
• MOAMap
• MOA (to be added)
• Visual MOA (to be added)
• MANUEL

Datasets

• Datasets used in GenGIS (Parks et al., Genome Research 2009)
• STAMP datasets
• Lateral genetic transfer in 144 genomes dataset (Beiko et al., Proc. Natl. Acad. Sci. 2005)
• Simulated data for 'The impact of reticulate evolution on genome phylogeny' (Beiko et al., Systematic Biology 2008) [to be added]

Contributors

• Robert Beiko
• Christian Blouin
• Donovan Parks
• Chris Whidden
• Norman MacDonald