fastDNAml
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FastDNAml
Cited in
(only showing first 100 items - show all)- Why neighbor-joining works
- A new quartet approach for reconstructing phylogenetic trees: Quartet joining method
- Invariants of phylogenies in a simple case with discrete states
- Distance measures in terms of substitution processes
- Inverting random functions
- What can and what cannot be inferred from pairwise sequence comparisons?
- Phylogenetic analysis of nucleotide sequences: An algebraic approach
- Bootstrapping a method of phylogenetic inference
- Probabilistic models in cluster analysis
- Regexpcount
- A phase transition for a random cluster model on phylogenetic trees.
- Phylogenetic inferences from molecular sequences: Review and critique
- Fast computation of maximum likelihood trees by numerical approximation of amino acid replacement probabilities
- Classification of molecular sequence data using Bayesian phylogenetic mixture models
- Phylogenetic estimation with partial likelihood tensors
- A stochastic evolution model for residue insertion-deletion independent from substitution
- Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph
- Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants
- Letter to editor: Rate-variation need not defeat phylogenetic inference through pairwise sequence comparisons
- A neutral evolution test derived from a theoretical amino acid substitution model
- Preface. Algebraic methods in phylogenetics
- Maximum likelihood estimation of symmetric group-based models via numerical algebraic geometry
- Lie-Markov models derived from finite semigroups
- Identifiability and reconstructibility of species phylogenies under a modified coalescent
- Inference in population genetics using forward and backward, discrete and continuous time processes
- A universal scaling law determines time reversibility and steady state of substitutions under selection
- An evolution model for sequence length based on residue insertion-deletion independent of substitution: an application to the GC content in bacterial genomes
- Lie Markov models
- Approximating likelihoods under low but variable rates across sites
- Landscapes on spaces of trees
- PAxML
- Modeling nucleotide evolution: A heterogeneous rate analysis
- PHYLIP
- MrBayes
- RAxML
- PAUP*
- Testing neutrality at copy-number-variable loci under the finite-allele and finite-site models
- An approximate stationary solution for multi-allele neutral diffusion with low mutation rates
- Dimensional reduction for the general Markov model on phylogenetic trees
- BIONJ
- MODELTEST
- Seq-Gen
- DNA sequence reconstruction based on innovated hybridization technique of probabilistic cellular automata and particle swarm optimization
- NAG4M2
- MEGA
- Mesquite
- An extended model for phylogenetic maximum likelihood based on discrete morphological characters
- A new method of finding component orthogonal arrays for order-of-addition experiments
- Optimal designs for order-of-addition experiments
- Gaphyl
- Lie Markov models with purine/pyrimidine symmetry
- CompLearn
- PhyML
- PAML
- Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret
- On the evolution rate in mammalian mitochondrial genomes
- Demographic inference under the coalescent in a spatial continuum
- Analytic solutions of maximum likelihood on forks of four taxa
- Cases in which ancestral maximum likelihood will be confusingly misleading
- SplitsTree
- Does random tree puzzle produce Yule-Harding trees in the many-taxon limit?
- A new molecular evolution model for limited insertion independent of substitution
- A note on probabilistic models over strings: the linear algebra approach
- BEAST
- BEAUti
- GPUTeraSort
- Entanglement invariants and phylogenetic branching
- Invertibility of the TKF model of sequence evolution
- Evolutionary rate variation and RNA secondary structure prediction
- rSPR
- Integer linear programming as a tool for constructing trees from quartet data
- Reconstruction of large phylogenetic trees: a parallel approach
- Minimum tree cost quartet puzzling
- Phyloquart
- A Bayesian approach to modelling reticulation events with application to the ribosomal protein gene rps11 of flowering plants
- The rise of statistical phylogenetics
- Omnibus CLTs for Fréchet means and nonparametric inference on non-Euclidean spaces
- Bali-phy
- IQ-TREE
- Bayesian estimation of the phylogeography of African gorillas with genome-differentiated population trees
- Matrix group structure and Markov invariants in the strand symmetric phylogenetic substitution model
- Heterogeneity in DNA multiple alignments: modeling, inference, and applications in motif finding
- NetNUMPAC
- A branch-price-and-cut algorithm for the minimum evolution problem
- T-REX
- ACEMD
- The Mathematics of Phylogenomics
- Hetero
- spr_neighbors
- RSEARCH
- Efficiently Calculating Evolutionary Tree Measures Using SAT
- MOLPHY
- Rec-I-DCM3
- CLUSTAG
- SEGM
- METREE
- Distinguishing phylogenetic networks
- SpectralTDF
- cBrother
- PhyME
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