• PHREEQC

  • Referenced in 19 articles [sw07853]
  • PHREEQC Version 3—A Computer Program for Speciation, Batch-Reaction, One-Dimensional Transport, and Inverse ... aqueous models, PHREEQC has capabilities for (1) speciation and saturation-index calculations; (2) batch-reaction...
  • PANTHER

  • Referenced in 15 articles [sw22973]
  • including inference of evolutionary events, such as speciation and gene duplication. Subfamilies are still curated...
  • diversitree

  • Referenced in 6 articles [sw26122]
  • evolution. Contains implementations of ’BiSSE’ (Binary State ’Speciation’ and Extinction) and its unresolved tree extensions ... MuSSE’ (Multiple State ’Speciation’ and Extinction), ’QuaSSE’, ’GeoSSE’, and ’BiSSE-ness’ Other included methods include ... continuous trait evolution and constant rate ’speciation’ and extinction...
  • PhyloNet

  • Referenced in 9 articles [sw20725]
  • such as horizontal gene transfer (HGT), hybrid speciation, and interspecific recombination, collectively referred...
  • ecceTERA

  • Referenced in 6 articles [sw24891]
  • loss and transfer (DTL) as well as speciation, involving sampled and unsampled lineages, within undated...
  • GEMS3K

  • Referenced in 4 articles [sw19058]
  • mass balance precision as that of conventional speciation codes. GEMS3K is already used in several...
  • phyloXML

  • Referenced in 4 articles [sw35271]
  • lengths, support values, and gene duplication and speciation events. Using these standardized elements allows interoperability...
  • TreeSim

  • Referenced in 2 articles [sw16856]
  • sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent ... page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim...
  • HyDe

  • Referenced in 2 articles [sw29663]
  • common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple ... population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available...
  • GIGA

  • Referenced in 3 articles [sw29606]
  • being composed of orthologous subtrees (containing only speciation events), which are joined by other evolutionary...
  • ORCHESTRA

  • Referenced in 2 articles [sw13426]
  • soil. ORCHESTRA (Object Representation of Chemical Speciation and Transport models) represents an entirely new approach...
  • Altruist

  • Referenced in 2 articles [sw32832]
  • shifts, Wright’s shifting balance, punctuated equilibria, speciation, and metaadaptation. The program runs...
  • SylvX

  • Referenced in 2 articles [sw34226]
  • recover co-diversification scenarios including co-speciation events, host-switches and extinctions. These evolutionary processes...
  • LEHGC

  • Referenced in 1 article [sw07856]
  • time and space and the chemical speciation at user-specified nodes...
  • MICROQL

  • Referenced in 1 article [sw23341]
  • BASIC language. The program calculates chemical speciation in aqueous solution at thermodynamic equilibrium...
  • WATSPEC

  • Referenced in 1 article [sw23343]
  • computer program for determining the equilibrium speciation of aqueous solutions...
  • GEMSFIT

  • Referenced in 1 article [sw25636]
  • Gibbs energy minimization (GEM) approach. This enables speciation-based fitting of complex solution systems such...
  • TESS

  • Referenced in 0 articles [sw18956]
  • biology entail estimating rates of lineage diversification (speciation–extinction) that are modeled using birth–death...
  • R

  • Referenced in 8180 articles [sw00771]
  • R is a language and environment for statistical...
  • SUNDIALS

  • Referenced in 209 articles [sw00927]
  • SUNDIALS was implemented with the goal of providing...