fastDNAml

swMATH6651MaRDI QIDQ18738FDOQ18738

Author name not available (Why is that?)

Described by source

• Adapting PAxML to the Hitachi SR8000-F1 Supercomputer

Cited In (87)

• Phylogenetic estimation with partial likelihood tensors
• Phylogenetic inferences from molecular sequences: Review and critique
• Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph
• Necessary and sufficient conditions for the existence of certain quadratic invariants under a phylogenetic tree
• Minimum tree cost quartet puzzling
• Approximating likelihoods under low but variable rates across sites
• Analytic solutions for three taxon ML trees with variable rates across sites
• The Mathematics of Phylogenomics
• A note on probabilistic models over strings: the linear algebra approach
• Experiments with the site frequency spectrum
• Fast computation of maximum likelihood trees by numerical approximation of amino acid replacement probabilities
• Letter to editor: Rate-variation need not defeat phylogenetic inference through pairwise sequence comparisons
• Multiple pattern matching: a Markov chain approach
• Phylogenetic distances for neighbour dependent substitution processes
• A phase transition for a random cluster model on phylogenetic trees.
• Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree
• Markov Bridges, Bisection and Variance Reduction
• Identifiability and reconstructibility of species phylogenies under a modified coalescent
• Demographic inference under the coalescent in a spatial continuum
• A stochastic evolution model for residue insertion-deletion independent from substitution
• An evolution model for sequence length based on residue insertion-deletion independent of substitution: an application to the \(GC\) content in bacterial genomes
• Unique reconstruction of tree-like phylogenetic networks from distances between leaves
• Reconstruction of large phylogenetic trees: a parallel approach
• An approximate stationary solution for multi-allele neutral diffusion with low mutation rates
• Using the tangle: A consistent construction of phylogenetic distance matrices for quartets
• Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model
• A new quartet approach for reconstructing phylogenetic trees: Quartet joining method
• A branch-price-and-cut algorithm for the minimum evolution problem
• Modeling nucleotide evolution: A heterogeneous rate analysis
• Why neighbor-joining works
• Distance measures in terms of substitution processes
• Phylogenetic analysis of nucleotide sequences: An algebraic approach
• What can and what cannot be inferred from pairwise sequence comparisons?
• Distinguishing Phylogenetic Networks
• Invariants of phylogenies in a simple case with discrete states
• Preface. Algebraic methods in phylogenetics
• A fast quartet tree heuristic for hierarchical clustering
• Closed form modeling of evolutionary rates by exponential Brownian functionals
• Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths
• Inverting random functions
• Distribution of distances between topologies and its effect on detection of phylogenetic recombination
• The EM algorithm and the rise of computational biology
• The minimum evolution problem: Overview and classification
• Evolutionary rate variation and RNA secondary structure prediction
• Lie Markov models
• Landscapes on spaces of trees
• Dimensional reduction for the general Markov model on phylogenetic trees
• Entanglement invariants and phylogenetic branching
• Bootstrapping a method of phylogenetic inference
• Analytic solutions of maximum likelihood on forks of four taxa
• Efficiently Calculating Evolutionary Tree Measures Using SAT
• Classification of molecular sequence data using Bayesian phylogenetic mixture models
• Polyhedral geometry of phylogenetic rogue taxa
• Lie Markov models with purine/pyrimidine symmetry
• Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
• Phase transition in the sample complexity of likelihood-based phylogeny inference
• On the dispersion index of a Markovian molecular clock
• A new molecular evolution model for limited insertion independent of substitution
• Assessing phenotypic correlation through the multivariate phylogenetic latent liability model
• Counting labeled transitions in continuous-time Markov models of evolution
• Mathematical models to reconstruct phylogenetic trees under the minimum evolution criterion
• Probabilistic models in cluster analysis
• A Bayesian approach to modelling reticulation events with application to the ribosomal protein gene rps11 of flowering plants
• Integer linear programming as a tool for constructing trees from quartet data
• Inference in population genetics using forward and backward, discrete and continuous time processes
• A neutral evolution test derived from a theoretical amino acid substitution model
• Title not available (Why is that?)
• Lie-Markov models derived from finite semigroups
• Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
• Heterogeneity in DNA Multiple Alignments: Modeling, Inference, and Applications in Motif Finding
• Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models
• Similar States in Continuous-Time Markov Chains
• Optimal designs for order-of-addition experiments
• Bayesian estimation of the phylogeography of African gorillas with genome-differentiated population trees
• A universal scaling law determines time reversibility and steady state of substitutions under selection
• The rise of statistical phylogenetics
• Some statistical methods for phylogenetic trees with application to HIV disease
• DNA sequence reconstruction based on innovated hybridization technique of probabilistic cellular automata and particle swarm optimization
• Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret
• Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants
• A new method of finding component orthogonal arrays for order-of-addition experiments
• Cases in which ancestral maximum likelihood will be confusingly misleading
• On the evolution rate in mammalian mitochondrial genomes
• Invertibility of the TKF model of sequence evolution
• An extended model for phylogenetic maximum likelihood based on discrete morphological characters
• Does random tree puzzle produce Yule-Harding trees in the many-taxon limit?
• Omnibus CLTs for Fréchet means and nonparametric inference on non-Euclidean spaces

This page was built for software: fastDNAml