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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

• SeqMonitor
• 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

Contributors

• Robert Beiko
• Christian Blouin
• Donovan Parks