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BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. (Source: Kent, W.J. 2002. BLAT -- The BLAST-Like Alignment Tool. Genome Research 4: 656-664. http://dx.doi.org/10.1101/gr.229202) BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome (but not the genome itself) in memory. Since the index takes up a bit less than a gigabyte of RAM, BLAT can deliver high performance on a reasonably priced Linux box.

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.

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).

Version 2 of the FASTA packages contains many programs for performing sequence comparisons, producing local alignments, and other related tasks for analysing DNA and proteins. Currently, the FASTA2 suite is in maintenance mode. This package provides the analysis tools from FASTA2. The searching programs are available in version 3 of the FASTA packages, which may be found in the port biology/fasta3. FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444- 2448, and W. R. Pearson (1990) "Rapid and Sensitive Sequence Comparison with FASTP and FASTA" Methods in Enzymology 183:63- 98). The FASTA2 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

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.

Fluctuate fits the model which has a single population which has been growing (or shrinking) according to an exponential growth law. It estimates 4Nu and g, where N is the effective population size, u is the neutral mutation rate per site, and g is the growth rate of the population. Fluctuate forms part of the Lamarc (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) suite. See: http://evolution.genetics.washington.edu/lamarc.html

LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) is a package of programs for computing population parameters such as population size, population growth rate and migration rates. It does this by using likelihoods for samples of data (sequences, microsatellites, and electrophoretic polymorphisms) from populations.

gff2ps is a script program developed with the aim of converting gff-formatted records into high quality one-dimensional plots in PostScript. Such plots maybe useful for comparing genomic structures and to visualizing outputs from genome annotation programs.

Gperiodic displays a periodic table of the elements, allowing you to browse through the elements, and view detailed information about each element.