• PoMo

  • Referenced in 8 articles [sw35039]
  • Based Approach for Species Tree Estimation. Incomplete lineage sorting can cause incongruencies of the overall ... that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic ... PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with...
  • ASTRAL-II

  • Referenced in 11 articles [sw20492]
  • have different trees due to incomplete lineage sorting, modeled by the multi-species coalescent model...
  • iGTP

  • Referenced in 5 articles [sw23050]
  • such as gene duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer...
  • SimPhy

  • Referenced in 5 articles [sw17058]
  • multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer...
  • OCTAL

  • Referenced in 2 articles [sw29609]
  • from the species tree due to incomplete lineage sorting, and estimated gene trees are completed ... useful technique for adding missing taxa to incomplete gene trees and provides good accuracy under ... accuracy can be reduced when incomplete lineage sorting is high, as the reference tree...
  • STELLS2

  • Referenced in 2 articles [sw32301]
  • given gene trees, which undergo incomplete lineage sorting (as illustrated in the above figure). STELLS...
  • Phylo-MCOA

  • Referenced in 2 articles [sw18727]
  • potentially interesting biological processes, such as incomplete lineage sorting, hybridization, and horizontal gene transfers. Here...
  • StarBEAST2

  • Referenced in 1 article [sw29665]
  • induces spurious substitution rate variation when incomplete lineage sorting is present. Another class of heuristics...
  • SVDquest

  • Referenced in 1 article [sw29619]
  • complicated by processes such as incomplete lineage sorting (ILS) that result in different loci having...
  • R

  • Referenced in 10196 articles [sw00771]
  • R is a language and environment for statistical...
  • PHYLIP

  • Referenced in 103 articles [sw07694]
  • PHYLIP is a free package of programs for...
  • MrBayes

  • Referenced in 62 articles [sw07715]
  • MrBayes: Bayesian Inference of Phylogeny. MrBayes is a...
  • RAxML

  • Referenced in 45 articles [sw07716]
  • Parallel inference of a 10.000-taxon phylogeny with...
  • PAUP*

  • Referenced in 57 articles [sw07834]
  • PAUP*: phylogenetic analysis under parsimony. PAUP* version 4.0...
  • BIONJ

  • Referenced in 30 articles [sw08301]
  • BIONJ: an improved version of the NJ algorithm...
  • Seq-Gen

  • Referenced in 32 articles [sw08310]
  • Seq-Gen. Sequence-Generator: An application for the...
  • Balibase

  • Referenced in 29 articles [sw08913]
  • BAliBASE: a benchmark alignment database for the evaluation...
  • HMMER

  • Referenced in 19 articles [sw10514]
  • HMMER web server: interactive sequence similarity searching. HMMER...
  • 3DCoffee

  • Referenced in 7 articles [sw12008]
  • 3DCoffee: combining protein sequences and structures within multiple...