Software & Downloads

The software packages on this page are (co)-developed by TRÊS members. Please refer to this URL when citing the software.

MLGsim 2.0

MLGsim 2.0 is an updated version of MLGsim (Stenberg et al. 2003). The program estimates the probability (P_sex ) that the frequency of a given Multilocus Genotype (MLG) (based on microsatellite marker data) is found in a randomly mating population. Using a simulation approach, the program estimates statistical significance values for these probabilities, given observed population allele frequencies.
MLGsim 2.0 differs from MLGsim in a number of important features:

• The program reads microsatellite data direct from a .txt file
• There is no longer a maximum sample size the program can handle
• Allele frequencies are now calculated by the program
• The bug encountered during longer simulations (memory leak) has been fixed
• The output has been extended with several new estimates

Downloads (right-click and select option "Save target as ..." to download):

• executable (MS-Windows)
• example input
• manual

R packages

• DAISIE package for R
  Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction.
• GUILDS package for R (Author: T. Janzen)
  Implementation of sampling formulas for the unified neutral model of biodiversity and biogeography, with or without guild structure.
• DAMOCLES package for R
  Simulation and likelihood methods for a dynamical community assembly that accounts for phylogenetic history.
• DDD package for R
  Calculates the likelihood of diversity-dependent diversification models for a given data set of branching times of a phylogenetic tree.
• PBD package for R
  Calculates the likelihood of the lineage-based protracted speciation model for a given data set of branching times of a phylogenetic tree.