From Bioinformatics.Org Wiki
Popular software for bioinformatics
Everyday bioinformatics is done with sequence search programs like BLAST, sequence analysis programs, like the EMBOSS and Staden packages, structure prediction programs like THREADER or PHD or molecular imaging/modelling programs like RasMol and WHAT IF.
- NetSurfP - Protein Surface Accessibility and Secondary Structure Predictions
- NetTurnP - Prediction of Beta-turn regions in protein sequences
- MODELLER - Used for homology or comparative modeling of protein three-dimensional structures
- AutoDock - Suite of Automated Docking Tools
- Gromacs - A molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids
- OrfPredictor - The OrfPredictor (ORF-Predictor) server is designed for ORF prediction and translation of a batch of EST or cDNA sequences
Popular Linux OS distributions for bioinformatics
- Gentoo Linux (List of bioinformatics packages)
- BioLinux (Based on Ubuntu 14.04)
- Ubuntu (Most of the packages found in BioLinux can be installed from the normal repositories).
Generic yet popular distributions: