SIB fastsimcoal2
University of Berne

fast sequential Markov coalescent simulation of genomic data under complex evolutionary models

Additional scrpts for the preparation of input files and the analysis of results

We list below a series of R and bash scripts that have been developed by several people from our group to facilitate the analysis of the results of fsc27 as well as for preparing input files.

visualizing scenarios modeled in par files

A new R script called ParFileViewer.r reads par files and plots the modeled scenario. parFileViewer has been adapter to reflect the latest chages in fsc27. this script can be useful to check that the  modeled scenario corresponds to what was intended.  It can also be useful to visualize the scenario obtained after some parameter estimation (use the *_maxL.par file). More information on the use of the this program can be found here.

shiny app

Alexandre Gouy has written a web application based on the R/Shiny framework h to facilitate the interpretation of fastsimcoal results. It features various visualisations: the demographic model, observed and expected marginal and joint SFS, as well as likelihood comparisons and parameter estimates dispersions if multiple runs are provided. Source code can be found gitHub. It can be used locally or directly from our CMPG web site.

running multiple instances of fsc

Laurent Excoffier and Nina Marchi have written a bash script to launch several instances of fsc under the SLURM worload manager. It requires .tpl, .est and .obs SFS files plus fastsimcoal program.
Vitor Sousa has written a similar bash script to run it on a single multi-core machine, with a an associated readme file here

processing demographic inference output

Several R scripts have been written by Vitor Sousa, Nina Marchi, and Laurent Excoffier to process the output of demographic inferences. They are found in the zip files  "" and "block bootstrap and model"

file converters

David Alexander Marques (DAM) , Vitor Sousa (VS), Nina Marchi (NM) and Laurent Excoffier (LE) have  written several file conversion scripts:

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Last updated by L. Excoffier on 15.04.2021
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