:: DESCRIPTION
CellScape is a visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CITUP is a bioinformatics tool that can be used to infer tumor heterogeneity using multiple samples from a single patient. Given mutational frequencies for each sample, CITUP uses an optimization based algorithm to find the evolutionary tree best explaining the data.
::DEVELOPER
Lab for Bioinformatics and Computational Genomics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Clonality Inference in Multiple Tumor Samples using Phylogeny.
Malikic S, McPherson AW, Donmez N, Sahinalp CS.
Bioinformatics. 2015 Jan 6. pii: btv003.
:: DESCRIPTION
BaTS (Bayesian Tip-Significance testing) is a package that allows the user to test for significant phylogeny-trait correlations whilst taking into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by Bayesian phylogenetics programs such as BEAST or MrBayes. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Parker J, Rambaut A, Pybus OG. 2008.
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty.
Infection, Genetics and Evolution 8:239-46
:: DESCRIPTION
phyloGenerator is an easy way for ecologists to make realistic, tenable phylogenies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
William D. Pearse, Andy Purvis
phyloGenerator: an automated phylogeny generation tool for ecologists
Methods in Ecology and Evolution Volume 4, Issue 7, pages 692–698,
:: DESCRIPTION
BAli-Phy is MCMC software for simultaneous Bayesian estimation of alignment and phylogeny (and other parameters).BAli-Phy can estimate phylogenetic trees from sequence data when the alignment is uncertain. Instead of conditioning on a single alignment estimate, BAli-Phy accounts for alignment uncertainty by integrating over all alignments. BAli-Phy does not rely on a guide tree because the alignment and the tree are co-estimated. Therefore it can construct phylogeny estimates of widely divergent sequences without bias toward a guide tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Suchard MA and Redelings BD
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny,
Bioinformatics, 22:2047-2048, 2006.
:: DESCRIPTION
HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environmen. HyPhy intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more
::DEVELOPER
Acme Computational Molecular Evolution Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005)
HyPhy: hypothesis testing using phylogenies.
Bioinformatics 21(5): 676-679
:: DESCRIPTION
PhyML (Phylogenetic estimation using Maximum Likelihood) is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology.
::DEVELOPER
Stéphane Guindon , Olivier Gascuel
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Systematic Biology, 59(3):307-21, 2010.
:: DESCRIPTION
ProteinEvolver generates samples of protein-coding genes and protein sequences evolved along phylogenies under structure-based substitution models. These models consider the protein structure to evaluate candidate mutations, which can be accepted (substitutions) or rejected depending on the energy of the protein structure of the mutated sequence.
::DEVELOPER
Unidad de Bioinformatica CBMSO
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Dec 1;29(23):3020-8. doi: 10.1093/bioinformatics/btt530. Epub 2013 Sep 12.
Protein evolution along phylogenetic histories under structurally constrained substitution models.
Arenas M1, Dos Santos HG, Posada D, Bastolla U.
:: DESCRIPTION
TransPhylo is a software package for the Bayesian inference of infectious disease transmission from a phylogeny.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mol Biol Evol. 2014 Jul;31(7):1869-79. doi: 10.1093/molbev/msu121. Epub 2014 Apr 8.
Bayesian inference of infectious disease transmission from whole-genome sequence data.
Didelot X, Gardy J, Colijn C
:: DESCRIPTION
Phy2HTML is a simple Python program that is designed to read a tree in Newick format and create a visualization of the tree for display in a webpage using only HTML and CSS.
::DEVELOPER
Michael S. Rosenberg’s Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
