Software at OSC |
Biosciences Software available at OSCAmber - a molecular simulation program bioperl - offers a set of perl modules which can be used for sequence manipulation BLAST - tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence BLAT - a sequence analysis tool which performs rapid mRNA/DNA and cross-species protein alignments bowtie - an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. ClustalW - a general purpose multiple sequence alignment program for DNA or proteins EMBOSS - a sequence analysis package specially developed for the needs of the molecular biology user community fitmodel - a program that estimates the parameters of various codon-based models of substitution HMMER - profile HMMs for protein sequence analysis MrBayes - a program for the Bayesian estimation of phylogeny NAMD - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems PAML - a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data Partek Pro* - an integrated, scalable software environment capable of analysis and transformation of millions of records or millions of variables PAUP -- a leading program for performing phylogenetic analysis for bioinformatics sequences RAxML - a fast implementation of maximum-likelihood phylogeny estimation that operates on both nucleotide and protein sequence alignments RECON - a package that performs de novo identification and classification of repeat sequence families from genomic sequences RepeatMasker - a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences Stata - a complete, integrated statistical package that provides everything needed for data analysis, data management, and graphics treebest - an original tree builder for constrained neighbour-joining and tree merge * Indicates software available through OSC's Statewide Software License Distribution Availability by machine
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