From Shiu Lab
Package of comp biol software
- A long list of bioinformatic resources from Anil Jegga, Cincinnati Children's Hospital Medical Center
- A comprehensive list from Glasglow.
- Genefinding.org: a very comprehensive collection of resources.
Sequence visualization and editing
- VisCoSe: Visualization and Comparison of Consensus Sequences
Multiple sequence alignemnt
- MEME: download section and installation instruction.
- SwissModel: web interface, no local version.
- msuprotein:many useful links for protein structure prediction.
- R: The R Project for Statistical Computing
- Bioconductor: an open source and open development software project for the analysis and comprehension of genomic data.
- BioC course: Very extensive tutorials on Bioconductor functionalities, from the Short Course ran at Bressanone, Italy in 2004
- R/BioC manual: From Thomas Girke, UC Riverside.
- Affymetrix tiling array tools: Integrated Genome Browser and Tiling Analysis Software from Affy.
- tilingArray: a Bioconductor package. Contain several functions available for finding segmentation patterns. Applied to a recently published paper.
- snapCGH: a Bioconductor package. The BioHMM module uses HMM to find segmentation patterns in CGH experiments, see the paper.
Transcription factor binding site
- IDEA: Graphical user interface for some commonly used software such as PAML and PHYLIP.
Ancestral state inference
- EvolveAGene: by Barry Hall
- modeler4simcoal2: a modeler for coalescent processes
- Cytoscape: an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.
- GenMAPP: a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes
- geWorkbench: genomics Workbench is a Java-based open-source platform for integrated genomics.
- Systems Biology Workbench: a software framework that allows heterogeneous application components-written in diverse programming languages and running on different platforms-to communicate and use each others' capabilities via a fast binary encoded-message system
- E-Cell: an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems, particularly focused on biological details of cellular behavior.