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CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.

Fast indexing and retrieval of FASTA records from flat file data bases.

Chemeq is a basic standalone filter written in C++ language, flex and bison. It takes strings like: 2H2 + O2 ---> 2 H2O and can output pretty LaTeX code, useful messages and much more. It aims to be embeddable in education tools.

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

Consed is a tool for viewing and editing sequence assemblies made by phrap, and includes Autofinish which will automatically choose finishing reads.

Free, open source molecular viewer and editor for protein structure, DNA structure, PDB, molecular rendering, biological macromolecule. Atoms may be drawn as spheres of different sizes. Bonds may be drawn as cylindrical sticks, conical sticks or as curved surfaces. Five types of slab are available: planar, spherical, semi-spherical, cylindrical and semi-cylindrical. The slab position and thickness are visible in a small window. Atomic bonds as well as atoms are treated as independent drawable objects. and more.

Crux is a software toolkit for molecular phylogenetic inference. It is structured as a set of Python modules, which makes it possible to quickly develop Python scripts that perform unique, non-canned analyses. Features include: * Tree log-likelihoods can be computed under a variety of models, including all specializations of GTR+I+G and mixture models. Tree likelihoods can be computed in parallel via pthreads. * Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis coupling) can sample among non-nested models using reversible model jumps. * Crux is capable of simulating character data under any model its likelihood engine is capable of. * The neighbor joining (NJ) and relaxed neighbor joining (RNJ) implementations are among the fastest in existence. * Pairwise distances between sequences can be computed based on percent identity, or using methods that correct for multiple hits (Jukes-Cantor, Kimura, and logDet).

DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.

fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML (part of his PHYLIP package). Users should consult the documentation for DNAML before using this program. fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C.

Simple and quick FastQ and FastA tool for file reading and conversion.