• fastDNAml

  • Referenced in 94 articles [sw06651]
  • fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. Much...
  • mboost

  • Referenced in 67 articles [sw07331]
  • component-wise (penalised) least squares estimates or regression trees as base-learners for fitting generalized...
  • CGAL

  • Referenced in 394 articles [sw00118]
  • simplification, subdivision and parameterization, as well as estimation of local differential properties, and approximation ... search structures (kd trees for nearest neighbor search, and range and segment trees), interpolation (natural...
  • ape

  • Referenced in 62 articles [sw04569]
  • alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path...
  • PoMo

  • Referenced in 8 articles [sw35039]
  • Allele Frequency-Based Approach for Species Tree Estimation. Incomplete lineage sorting can cause incongruencies ... incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach ... this model to perform efficient estimation of species trees. We test the performance of PoMo ... well suited for genome-wide species tree estimation and that on such data...
  • PAML

  • Referenced in 43 articles [sw10916]
  • good for tree making. It may be used to estimate parameters and test hypotheses...
  • VineCopula

  • Referenced in 40 articles [sw08160]
  • copula selection and (vine) tree construction. Models can be estimated either sequentially or by joint...
  • ASTRAL-II

  • Referenced in 11 articles [sw20492]
  • ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands ... estimation of species phylogenies requires multiple loci, since different loci can have different trees...
  • STEM-hy

  • Referenced in 7 articles [sw23618]
  • STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Summary: STEM ... obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees...
  • iGLASS

  • Referenced in 4 articles [sw29611]
  • improvement to the GLASS method for estimating species trees from gene trees. Several methods have ... these methods provide consistent species tree topology estimates under a standard model, most either ... Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast ... divergence times, leading to biased estimates of species tree branch lengths. By assuming a multispecies...
  • ASTRID

  • Referenced in 6 articles [sw23620]
  • aware tool for species tree estimation. ASTRID runs in two phases: a distance matrix ... computed from the input gene trees, a distance-based method is used to compute...
  • MUSCLE

  • Referenced in 75 articles [sw13193]
  • Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using ... expectation score, and refinement using tree‐dependent restricted partitioning. The speed and accuracy of MUSCLE...
  • TERA

  • Referenced in 4 articles [sw34318]
  • trees. Results: Here, we present the Tree Estimation using Reconciliation (TERA) algorithm, a parsimony based ... species tree aware method for gene tree reconstruction based on a scoring scheme combining duplication ... with an estimate of the sequence likelihood. TERA explores all reconciled gene trees that...
  • DeBaCl

  • Referenced in 3 articles [sw23572]
  • Interactive DEnsity-BAsed CLustering. The level set tree approach of Hartigan (1975) provides a probabilistically ... level sets of a density estimator, this approach offers many advantages for exploratory analysis ... packages exist for level set tree estimation, but their practical usefulness is limited by computational ... illustrate how DeBaCl’s level set tree estimates can be used for difficult clustering tasks...
  • SuperFine

  • Referenced in 3 articles [sw29605]
  • supertree estimation. Many research groups are estimating trees containing anywhere from a few thousands ... eventual goal of the estimation of a Tree of Life, containing perhaps as many ... this range. One approach to estimate a large species tree is to use phylogenetic estimation ... trees on subsets of the taxa, are important tools for phylogeny estimation where phylogenetic analyses...
  • phytools

  • Referenced in 14 articles [sw10003]
  • functions for Bayesian and ML ancestral state estimation; visual simulation of trait evolution; fitting models ... rate of character evolution on the tree; fast Brownian motion simulation and simulation under several ... tree with singleton nodes and one character state per edge; estimating a phylogeny using...
  • erboost

  • Referenced in 10 articles [sw26258]
  • Expectile regression is a nice tool for estimating the conditional expectiles of a response variable ... This package implements a regression tree based gradient boosting estimator for nonparametric multiple expectile regression...
  • OCTAL

  • Referenced in 2 articles [sw29609]
  • sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they ... incomplete lineage sorting, and estimated gene trees are completed using OCTAL with ... reference tree based on a species tree estimated from the multi-locus dataset. OCTAL produces ... similar the reference tree (typically an estimated species tree) is to the true gene tree...
  • bnlearn

  • Referenced in 77 articles [sw08265]
  • independence tests. The Naive Bayes and the Tree-Augmented Naive Bayes (TAN) classifiers are also ... included, as well as support for parameter estimation (maximum likelihood and Bayesian) and inference, conditional...
  • phangorn

  • Referenced in 8 articles [sw08311]
  • Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony...