• ASTRAL-II

  • Referenced in 11 articles [sw20492]
  • ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands ... lineage sorting, modeled by the multi-species coalescent model. We recently developed a coalescent-based ... statistically consistent under the multi-species coalescent model and which is more accurate than other ... coalescent-based methods on the datasets we examined. ASTRAL runs in polynomial time, by constraining...
  • MixGHD

  • Referenced in 14 articles [sw18474]
  • convex contour plots. The ’MCGHD’, mixture of coalesced generalized hyperbolic distributions is a new more...
  • GKLEE

  • Referenced in 11 articles [sw12794]
  • often do not target performance bugs (non-coalesced memory accesses, memory bank conflicts, and divergent...
  • STEM-hy

  • Referenced in 7 articles [sw23618]
  • using maximum likelihood for gene trees under coalescence. Summary: STEM is a software package written ... sample of gene trees under the coalescent model. It includes options to compute...
  • MSMS

  • Referenced in 7 articles [sw34261]
  • MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus ... Motivation: We have implemented a coalescent simulation program for a structured population with selection...
  • CompactCH

  • Referenced in 5 articles [sw34255]
  • gene tree probability under the multispecies coalescent and its application in the inference of population ... based on the notion of compact coalescent histories: multiple coalescent histories are represented ... single compact coalescent history. The key advantage of our new algorithm is that it runs...
  • fastsimcoal

  • Referenced in 6 articles [sw35122]
  • fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Motivation ... technological advances. We present here a new coalescent-based simulation program fastsimcoal, which is able...
  • iGTP

  • Referenced in 5 articles [sw23050]
  • duplication and loss, incomplete lineage sorting (deep coalescence), and horizontal gene transfer. Gene tree parsimony ... under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves ... using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient...
  • PoMo

  • Referenced in 8 articles [sw35039]
  • other approaches, our model does not use coalescent theory but is allele frequency based...
  • LAMARC

  • Referenced in 7 articles [sw11443]
  • successor programs to the older programs Coalesce, Fluctuate, and Recombine, which are no longer being...
  • BUCKy

  • Referenced in 7 articles [sw23619]
  • population tree with branch lengths in coalescent units is estimated from quartet concordance factors. Availability...
  • phylodyn

  • Referenced in 4 articles [sw19813]
  • effective population size trajectory. We assume the coalescent and the sequentially Markov coalescent processes ... generative models of genealogies. We include several coalescent simulation functions that are useful for testing...
  • PyCBC

  • Referenced in 6 articles [sw23194]
  • waves. It contains algorithms that can detect coalescing compact binaries and measure the astrophysical parameters...
  • iGLASS

  • Referenced in 4 articles [sw29611]
  • tree branch lengths. By assuming a multispecies coalescent model in which multiple lineages are sampled ... waiting time until the first interspecific coalescence occurs between the two taxa, considering all loci...
  • MSCquartets

  • Referenced in 4 articles [sw34523]
  • Gene Tree Quartets under the Multi-Species Coalescent. Methods for analyzing and using quartets displayed ... tree or network under the multi-species coalescent model. These include quartet hypothesis tests...
  • FTEC

  • Referenced in 3 articles [sw24692]
  • FTEC: A coalescent simulator for modeling faster than exponential growth. SUMMARY: Recent genetic studies ... introduce FTEC, an easy-to-use coalescent simulation program capable of simulating haplotype samples drawn...
  • msBayes

  • Referenced in 3 articles [sw24735]
  • approximate Bayesian computation (ABC) under a hierarchical coalescent model to test for simultaneous divergence ... parameters (sub-parameters) that can affect the coalescent. msBayes is a software package consisting...
  • Recodon

  • Referenced in 3 articles [sw35372]
  • Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. Results: We introduce ... coalescent program, called Recodon, which is able to simulate samples of coding DNA sequences under...
  • pegas

  • Referenced in 4 articles [sw08307]
  • population nucleotide sequences and micro-satellites including coalescence analyses...
  • KBLAS

  • Referenced in 4 articles [sw17481]
  • BLAS API. Another optimization technique allows ensuring coalesced memory access when dealing with submatrices, especially...