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Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file.

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

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).

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.

Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and one program (prss3) for evaluating statistical significance from randomly shuffled sequences. Several additional analysis programs, including programs that produce local alignments, are available as part of version 2 of the FASTA package, which is available as the port biology/fasta. FASTA is described in: W. R. Pearson and D. J. Lipman (1988), "Improved Tools for Biological Sequence Analysis", PNAS 85:2444-2448; W. R. Pearson (1996) "Effective protein sequence comparison" Meth. Enzymol. 266:227-258; Pearson et. al. (1997) Genomics 46:24-36; Pearson, (1999) Meth. in Molecular Biology 132:185-219. The FASTA3 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.

MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

MUSCLE is multiple alignment software for protein and nucleotide sequences. The name stands for multiple sequence comparison by log-expectation. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in the published tests. MUSCLE can achieve both better average accuracy and better speed than CLUSTALW or T-Coffee, depending on the chosen options. Citation: Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797. Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113. The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper.

This package implements the Sim4 algorithm for aligning expressed DNA with genomic sequences, described in the paper: L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998) "A computer program for aligning a cDNA sequence with a genomic DNA sequence." Genome Research 8, 967-974. Port maintained by the FreeBSD bio-porters mailing list.