:: DESCRIPTION
bioscripts.convert provides scripts that use Biopython internally to simply convert multiple files on the commandline.
::DEVELOPER
Paul-Michael Agapow and Austin Burt (a.burt@imperial.ac.uk), Dept. Biology, University College London
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
NGS-MC is an R package which calculates the statistics and estimators in a Markov sequence model including the effective coverage, a chi-square statistic for k-words, normal approximation for every k-word, and five estimators for the order of Markov chain from NGS short read data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Charles H. Cannon, Fengzhu Sun (2015),
Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics.
Bioinformatics. 2015 Jun 30. pii: btv395.
:: DESCRIPTION
BEAST (Bayesian Evolutionary Analysis Samling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
BEAST 2 is an open source cross-platform program for Bayesian MCMC phylogenetic analysis of molecular sequences.
::DEVELOPER
The University of Auckland Computational Evolution Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ.
PLoS Comput Biol. 2019 Apr 8;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650.
Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration.
Gavryushkina A, Welch D, Stadler T, Drummond AJ.
PLoS Comput Biol. 2014 Dec 4;10(12):e1003919. doi: 10.1371/journal.pcbi.1003919.
Alexei J Drummond and Andrew Rambaut
BEAST: Bayesian evolutionary analysis by sampling trees
BMC Evolutionary Biology 2007, 7:214doi:10.1186/1471-2148-7-214
:: DESCRIPTION
TREEFINDER computes phylogenetic trees from molecular sequences.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Jobb, G., A. von Haeseler, and K. Strimmer.
TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics
BMC Evol Biol. 2004 Jun 28;4:18.
:: DESCRIPTION
GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned nucleotide, codon and amino acid data sets using the maximum likelihood criterion. On a practical level, the program is able to perform maximum-likelihood tree searches on large data sets in a number of hours.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
