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Explore, manipulate, analyze, and simulate phylogenetic objects (alignments, trees, and MCMC logs) J.W. Brown, J.F. Walker, and S.A. Smith POY A phylogenetic analysis program that supports multiple kinds of data and can perform alignment and phylogeny inference. A variety of heuristic algorithms have been developed for this purpose
Databases for oncogenomic research are biological databases dedicated to cancer data and oncogenomic research. They can be a primary source of cancer data, offer a certain level of analysis (processed data) or even offer online data mining.
Methods (implemented by each program) that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. [2]
MrBayes is a free software tool that performs Bayesian inference of phylogeny. It was originally written by John P. Huelsenbeck and Frederik Ronquist in 2001. [28] As Bayesian methods increased in popularity, MrBayes became one of the software of choice for many molecular phylogeneticists.
These detection methods generate terabytes of data per experiment. The data is often found to contain considerable variability, or noise, and thus Hidden Markov model and change-point analysis methods are being developed to infer real copy number changes. [citation needed] Two important principles can be used to identify cancer by mutations in ...
Phylogenetic trees generated by computational phylogenetics can be either rooted or unrooted depending on the input data and the algorithm used. A rooted tree is a directed graph that explicitly identifies a most recent common ancestor (MRCA), [citation needed] usually an inputed sequence that is not represented in the input.
A phylogenetic convolutional neural network (Ph-CNN) is a convolutional neural network architecture proposed by Fioranti et al. in 2018 to classify metagenomics data. [19] In this approach, phylogenetic data is endowed with patristic distance (the sum of the lengths of all branches connecting two operational taxonomic units [OTU]) to select k ...
Tanagra is a free suite of machine learning software for research and academic purposes developed by Ricco Rakotomalala at the Lumière University Lyon 2, France. [1] [2] Tanagra supports several standard data mining tasks such as: Visualization, Descriptive statistics, Instance selection, feature selection, feature construction, regression, factor analysis, clustering, classification and ...