EggLib version 2.1 is archived.

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eggcoal is a standalone program for generating samples under the coalescent framework. It is based on the egglib-cpp C++ library. It can be used independently from the rest of the package. It is based on the same assumptions as the ms software and uses the same rescaling of time units (time is counted in 4N generations, where N is the number of diploid individuals in the populations). It also generates compatible output files. Here is a list of features provided by eggcoal:

  • Haploid (1 gene) and/or diploid (2 genes per individual) samples.
  • Partial selfing (panmixy is of course also allowed).
  • Recombination (but not gene conversion and no variation of recombination rate along the sequence yet).
  • Variation of population size.
  • Population structure and arbitrary migration matrices.
  • Exponential population growth or decline.
  • Change of all migration rates in the past.
  • Change of the selfing rate in the past.
  • Change of the exponential growth/decline rate in the past.
  • Instant population change.
  • Population fusion or split.
  • Composite bottleneck model (with one-parameter intensity combining duration and population size reduction).
  • Standard infinite site mutation model.
  • Finite site mutation models (with variation of site mutability).
  • Possibility to set site locations (having effect on the recombination rate between them).
  • Fixed number of mutations.
  • Mutation models: finite allele model, infinite allele model, stepwise mutation model, two-phase mutation model.
  • Microsatellite are exported in a slightly different format to accomodate allele values larger than 9.
  • Possibility to implement mutation bias (e.g. transition vs. transversion).
  • Generate fasta alignments.
  • Generate newick trees (also for simulations with recombination).
  • Output simulation statistics (not diversity statistics; for those, use a program such as eggstats).

Once the program is installed, type eggcoal -h for a short manual page and eggcoal -u for a longer manual.

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