A few of the more widespread and versatile programming languages popular in the sciences. Download info and tutorials available through the links provided.
R is a GNU environment for statistical computing (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, …) and graphics.
MATLAB is a commercial data analysis and numerical simulation package that can be used for many things, including financial calculations, curve fitting, image processing, statistics, and signal analysis. Brandeis has a full site license.
Page of tools for analyzing the alignment of three or more biological sequences (protein or nucleic acid) of similar length. From the output, homology can be inferred and the evolutionary relationships between the sequences studied.
Finds regions of similarity between biological sequences. Compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
"The last alignment program you'll ever need"
Allows hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks.
Open source platform designed for gene analysis and discovery. Bioinformatcs tools for gene discovery and prediction of biological function of genes are developed by community experts, curated for quality, and monitored for functionality..
Database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and non-polymorphic variants.
Vector Alignment Search Tool: identify similar protein 3-dimensional structures by purely geometric criteria, and identify distant homologs that cannot be recognized by sequence comparison.
Provides tools for the analysis and comprehension of high-throughput genomic data. Uses the R statistical programming language, and is open source and open development.
GenePattern provides hundreds of analytical tools for the analysis of gene expression (RNA-seq and microarray), sequence variation and copy number, proteomic, flow cytometry, and network analysis. These tools are all available through a Web interface with no programming experience required.
Database for Annotation, Visualization and Integrated Discovery: web-accessible programs, functional annotation tools for investigators to understand biological meaning behind large list of genes.
Cn3D ("see in 3D"): web-based app to view 3-dimensional structures from NCBI's Entrez Structure database. Windows, Mac, Unix compatible. Simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features.
Open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
