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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.

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

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.

Visualizing the results of molecular orbital calculations 1) MO program: gaussian, gamess, mopac, etc. 2) display molecule in 3D: geo-opt, single-point, nomal mode (animation) 3) density: contour plot or 3D view for electron density and MO coefficient Everything what you want about MO calculation can be seen. By the distribution policy of the author; * Only the latest version is supplied. * Users must get the `distfiles' from the original site. * Do not re-distribute the source and the executable. * Using a not-so-latest version is prohibited, because the author may only respond about the latest version.

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.

A standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.

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

GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms This suite of programs implements the approach to phylogeny reconstruction from gene orders described in the paper Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., and Yan, M., ``A detailed study of breakpoint analysis,'' Proc. 6th Pacific Symp. Biocomputing PSB 2001, Hawaii (2001). In its current state, "grappa" allows one to explore either the space of all possible trees on n labelled leaves or the space of all such trees that obey (are refinements of) a particular constraint tree. "invdist" takes the first two genomes in the input file and returns their inversion distance. "distmat" prints the inversion and breakpoint distance matrices.

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.