fastDNAml

swMATH6651MaRDI QIDQ18738FDOQ18738

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Official website: https://www.life.illinois.edu/gary/programs/fastDNAml.html

Described by source

• Adapting PAxML to the Hitachi SR8000-F1 Supercomputer

Cited In (only showing first 100 items - show all)

• Phylogenetic inferences from molecular sequences: Review and critique
• Approximating likelihoods under low but variable rates across sites
• A neutral evolution test derived from a theoretical amino acid substitution model
• Fast computation of maximum likelihood trees by numerical approximation of amino acid replacement probabilities
• Lie-Markov models derived from finite semigroups
• Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
• Phylogenetic distances for neighbour dependent substitution processes
• Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models
• A stochastic evolution model for residue insertion-deletion independent from substitution
• SpaceMix
• 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
• An evolution model for sequence length based on residue insertion-deletion independent of substitution: an application to the \(GC\) content in bacterial genomes
• An approximate stationary solution for multi-allele neutral diffusion with low mutation rates
• Some statistical methods for phylogenetic trees with application to HIV disease
• Modeling nucleotide evolution: A heterogeneous rate analysis
• Phylogenetic analysis of nucleotide sequences: An algebraic approach
• Identifiability of a coalescent-based population tree model
• Preface. Algebraic methods in phylogenetics
• Closed form modeling of evolutionary rates by exponential Brownian functionals
• Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths
• DNA sequence reconstruction based on innovated hybridization technique of probabilistic cellular automata and particle swarm optimization
• Distribution of distances between topologies and its effect on detection of phylogenetic recombination
• The EM algorithm and the rise of computational biology
• Evolutionary rate variation and RNA secondary structure prediction
• 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
• Bootstrapping a method of phylogenetic inference
• On the evolution rate in mammalian mitochondrial genomes
• On the dispersion index of a Markovian molecular clock
• A new molecular evolution model for limited insertion independent of substitution
• Counting labeled transitions in continuous-time Markov models of evolution
• Invertibility of the TKF model of sequence evolution
• An extended model for phylogenetic maximum likelihood based on discrete morphological characters
• Heterogeneity in DNA multiple alignments: modeling, inference, and applications in motif finding
• 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
• Phylogenetic estimation with partial likelihood tensors
• 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
• 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
• Letter to editor: Rate-variation need not defeat phylogenetic inference through pairwise sequence comparisons
• Multiple pattern matching: a Markov chain approach
• 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
• Unique reconstruction of tree-like phylogenetic networks from distances between leaves
• Reconstruction of large phylogenetic trees: a parallel approach
• 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
• Why neighbor-joining works
• Distance measures in terms of substitution processes
• What can and what cannot be inferred from pairwise sequence comparisons?
• Regexpcount
• PAxML
• Invariants of phylogenies in a simple case with discrete states
• MrBayes
• PHYLIP
• RAxML
• PAUP*
• BIONJ
• BEAST
• MODELTEST
• Seq-Gen
• NAG4M2
• MEGA
• Mesquite
• Gaphyl
• CompLearn
• PAML
• PhyML
• BEAUti
• GPUTeraSort
• SplitsTree
• A fast quartet tree heuristic for hierarchical clustering
• rSPR
• Phyloquart
• Bali-phy
• IQ-TREE
• NetNUMPAC
• ACEMD
• T-REX
• Hetero
• RSEARCH
• spr_neighbors
• MOLPHY
• Rec-I-DCM3

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