• fastsimcoal

  • Referenced in 6 articles [sw35122]
  • fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Motivation...
  • iGLASS

  • Referenced in 4 articles [sw29611]
  • times, leading to biased estimates of species tree branch lengths. By assuming a multispecies coalescent ... distribution of the waiting time until the first interspecific coalescence occurs between the two taxa...
  • SupStable.jl

  • Referenced in 3 articles [sw34616]
  • steps taken backwards in time before the coalescence is detected is finite. We analyse...
  • ASTRAL-II

  • Referenced in 9 articles [sw20492]
  • other coalescent-based methods on the datasets we examined. ASTRAL runs in polynomial time...
  • CompactCH

  • Referenced in 4 articles [sw34255]
  • histories are represented by a single compact coalescent history. The key advantage ... algorithm is that it runs in polynomial time in the number of gene lineages...
  • MSMS

  • Referenced in 7 articles [sw34261]
  • single locus. Motivation: We have implemented a coalescent simulation program for a structured population with ... adds a model for deme- and time-dependent selection using forward simulations. The program...
  • msBayes

  • Referenced in 3 articles [sw24735]
  • approximate Bayesian computation (ABC) under a hierarchical coalescent model to test for simultaneous divergence ... characterize the degree of variability in divergence times across co-distributed population pairs while allowing ... parameters (sub-parameters) that can affect the coalescent. msBayes is a software package consisting...
  • iGTP

  • Referenced in 3 articles [sw23050]
  • under the duplication, duplication-loss, and deep coalescence reconciliation costs. iGTP significantly extends and improves ... results. CONCLUSIONS: iGTP enables, for the first time, gene tree parsimony analyses of thousands ... using the duplication, duplication-loss, and deep coalescence reconciliation costs, all from within a convenient...
  • LIFT

  • Referenced in 3 articles [sw20596]
  • tracking system, called LIFT, which minimizes run-time overhead by exploiting dynamic binary instrumentation ... aggressively eliminates unnecessary dynamic information flow tracking, coalesces information checks, and efficiently switches between target ... only 6.2% for server applications, and 3.6 times on average for seven SPEC INT2000 applications...
  • FTEC

  • Referenced in 3 articles [sw24692]
  • introduce FTEC, an easy-to-use coalescent simulation program capable of simulating haplotype samples drawn ... that has maintained a constant size over time. AVAILABILITY: Source code for FTEC is freely...
  • phylodyn

  • Referenced in 3 articles [sw19813]
  • isochronous sampling) or at different points in time (heterochronous sampling); in addition, sampling events ... effective population size trajectory. We assume the coalescent and the sequentially Markov coalescent processes...
  • msPar

  • Referenced in 1 article [sw23325]
  • version (hereafter referred as “msPar”) of the coalescent simulation program ms, providing the same functionality ... knowledge this is the first time such parallelization has been applied to ms, and shown ... cluster, performing up to 42 times faster than original ms when using 72 logical processors ... other simulators using approximations to the standard coalescent approach. Source code is available...
  • BLNN

  • Referenced in 1 article [sw32579]
  • Bayesian Learning for Neural Networks (BLNN) package coalesces the predictive power of neural networks with ... Bayesian sampling techniques for the first time in R. BLNN offers users Hamiltonian Monte Carlo...
  • Recodon

  • Referenced in 3 articles [sw35372]
  • demography. Results: We introduce a new coalescent program, called Recodon, which is able to simulate ... implemented is an extension to the general time-reversible model of nucleotide substitution with...
  • TreeSim

  • Referenced in 2 articles [sw16856]
  • through time. (i) For sampling at one time point, simulations are performed under a constant ... exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees...
  • ARGON

  • Referenced in 1 article [sw34268]
  • fast, whole-genome simulation of the discrete time Wright-fisher process. Results: We present ... superior to currently available methods for coalescent simulation. The simulator supports arbitrary demographic history, migration...
  • scrm

  • Referenced in 0 articles [sw18176]
  • neutral models of evolution. Different to other coalescent based simulations, it has an optional approximation ... high accuracy while maintaining a linear run time cost for long sequences. It is optimized...
  • StarBEAST2

  • Referenced in 1 article [sw29665]
  • estimates of substitution rates. Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees ... tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when...
  • libcloudph++

  • Referenced in 1 article [sw37978]
  • particle-based scheme with Monte-Carlo coalescence. The three schemes are intended for modelling frameworks ... dimensional analysis of the code at compile time. The particle-based scheme is implemented using...
  • WarpDrive

  • Referenced in 1 article [sw35093]
  • their compact data layout and expected constant time complexity for insertion and querying. However, associated ... novel subwarp-based probing scheme featuring coalesced memory access over consecutive memory regions in order...