• PoMo

  • Referenced in 7 articles [sw35039]
  • Allele Frequency-Based Approach for Species Tree Estimation. Incomplete lineage sorting can cause incongruencies ... possible to incur several biases in species tree estimation. Here, we present a simple maximum ... 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...
  • ASTRAL-II

  • Referenced in 9 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 5 articles [sw23620]
  • aware tool for species tree estimation. ASTRID runs in two phases: a distance matrix ... input gene trees, a distance-based method is used to compute a species tree from...
  • ecceTERA

  • Referenced in 6 articles [sw24891]
  • binary species trees and binary gene trees. Moreover, ecceTERA can estimate accurate species-tree aware...
  • OCTAL

  • Referenced in 2 articles [sw29609]
  • sampling, and gene birth and loss), estimated gene trees are often incomplete, meaning that they ... contain all of the species of interest. As incomplete gene trees can impact downstream analyses ... estimated gene trees are completed using OCTAL with a reference tree based on a species ... similar the reference tree (typically an estimated species tree) is to the true gene tree...
  • SuperFine

  • Referenced in 3 articles [sw29605]
  • thousands of species, toward the eventual goal of the estimation of a Tree of Life ... this range. One approach to estimate a large species tree is to use phylogenetic estimation...
  • SVDquest

  • Referenced in 1 article [sw29619]
  • SVDquest: Improving SVDquartets species tree estimation using exact optimization within a constrained search space. pecies ... having different trees. Summary methods, which estimate species trees by combining gene trees, are popular ... estimate the species tree, and so are not impacted by gene tree estimation issues ... ability to reconstruct species trees without needing to estimate accurate gene trees. We present SVDquest...
  • StarBEAST2

  • Referenced in 1 article [sw29665]
  • StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates. Fully Bayesian ... multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands ... tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence ... enable accurate estimates of per-species substitution rates, we introduce species tree relaxed clocks...
  • DynaDup

  • Referenced in 1 article [sw33126]
  • tree parsimony for incomplete gene trees. Species tree estimation from gene trees can be complicated ... parsimony” (GTP) is one approach for estimating species trees from multiple gene trees...
  • SIESTA

  • Referenced in 1 article [sw29618]
  • optimal supertrees and species trees. Background: Many supertree estimation and multi-locus species ... tree estimation methods compute trees by combining trees on subsets of the species set based ... criterion. A recent approach to computing large trees has been to constrain the search space ... optimal solutions in polynomial time. Several phylogenomic estimation methods, such as ASTRAL, the MDC algorithm...
  • NJMerge

  • Referenced in 1 article [sw29612]
  • scaling phylogeny estimation methods and its application to species trees. NJMerge is a tool ... scaling phylogengy estimation methods to large datasets. NJMerge can be used in a divide ... divide the species set into disjoint subsets, 2) construct trees on each subset ... sucessfully tested in the context of species tree estimation (Molloy and Warnow...
  • TERA

  • Referenced in 4 articles [sw34318]
  • algorithm, a parsimony based, species tree aware method for gene tree reconstruction based ... with an estimate of the sequence likelihood. TERA explores all reconciled gene trees that ... amalgamated from a sample of gene trees. Using a large scale simulated dataset, we demonstrate ... find that incorporating knowledge of the species tree results in a two thirds reduction...
  • STELLS2

  • Referenced in 1 article [sw32301]
  • based maximum likelihood inference of species trees from gene tree topologies. STELLS is a program ... finding the maximum likelihood estimate of the species tree for the given gene trees, which...
  • Phybase

  • Referenced in 1 article [sw18999]
  • read, write, manipulate, simulate, estimate, summarize and plot species trees, which contain not only...
  • phytools

  • Referenced in 14 articles [sw10003]
  • species. For example, the package includes functions for Bayesian and ML ancestral state estimation; visual ... rate of character evolution on the tree; fast Brownian motion simulation and simulation under several...
  • CAFE

  • Referenced in 3 articles [sw12375]
  • tree, and given the gene family sizes in the extant species, CAFE can estimate...
  • EPoS

  • Referenced in 5 articles [sw08375]
  • software framework for phylogenetic analysis. Estimating Phylogenies of Species (EPoS) is a modular software framework ... known phylogenetic algorithms and a multitude of tree visualization methods and layouts. Implemented algorithms cover...
  • FastRFS

  • Referenced in 2 articles [sw29617]
  • from trees computed on subsets, are critically important tools for enabling the statistical estimation ... large and potentially heterogeneous datasets. Supertree estimation is itself NP-hard, and no current supertree ... designed for, containing thousands of species and many subset trees. Results: We present FastRFS...