mimicree2 Wiki

Genome-wide forward simulations of evolving populations

Brought to you by: chrvla, rokofler

ReleaseNotes

Authors:

new feature: sex specific fitness functions for the qff-mode; for example, males could have a different phenotypic optimum than females

fixed a bug in arbitrary fitness function; binary search generated an error message

improved the command line help; ordered parameters into mandatory, semi-mandatory and optional; provided example usage; and added a note to --output-dir that the directory needs to exist

all file parsers now accept \s+ as delimiter of columns (before it was tab: \t); that is at least one of both space or tabulator is accepted; this change should enhance usability while still preserving backwards compatibility

unit tests for reading haploid files
minimum population size for clonal evolution reduced to 1; population dies out only if no sex partners are found

new feature: conversion from arp-files (eg fastsimcoal and Arlequin) to Mimicree2 haplotypes

new feature: Added support for simulations of haploids
new feature: Added support for simulation of clonal evolution (both haploids and diploids are supported)
a recombination file is not required anymore; if no recombination file is provided a default recombination rate of zero is assumed
haplotype files now accept both tab and space as column separators
the output of hemizygous sex chromosomes was improved; now only one haploid genome is written (previously it was two

implemented feature requested by a user: the minimum size of a sexual population is now 2; one male and female (before it was three..)

implemented feature requested by a user: different snapshots are now possible for the sync, haplotypes, and fitness, i.e. the generations at which output is requested may differ between sync, haplotypes and fitness