From Bioinformatics Software
Welcome to the Bioinformatics Software and Resources page.
Key: P = phylogenetics, S = statistics, B = biogeography, V = visualization, G = genomics, M = metagenomics, L = lateral genetic transfer, A = sequence alignment
- 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)
- EvolSimulator: a simulation test bed for hypotheses of genome evolution. (PL)
- Express Beta Diversity (EBD): taxon- and phylogenetic-based beta diversity measures. (P)
- Fragment classification package (FCP): Homology- and composition-based classifiers for assigning a taxonomic attribution to metagenomic fragments. (GML)
- GANN: a machine learning method designed with the complexities of transcriptional regulation in mind.
- 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)
- Network Diversity: calculation of beta diversity over phylogenetic networks. (P)
- 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)
- 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)
- VAREB [to be added]
- WOOF: a tool designed to rigourously apply the principle of visual alignment validation. (SA)
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- 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]