visits since March 2011

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

While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure.

fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations.

Different markers, such as DNA sequences, SNPs, STRs (microsatellites) or multi-locus allelic data can be generated under a variety of mutation models (e.g. finite- and infinite-site models for DNA sequences, stepwise or generalized stepwise mutation model for STRs data, infinite-allele model for standard multi-allelic data).

fastsimcoal can simulate data in genomic regions with arbitrary recombination rates, thus allowing for recombination hotspots of different intensities at any position. fastsimcoal implements a new approximation to the ancestral recombination graph in the form of sequential Markov coalescent allowing it to very quickly generate genetic diversity for >100 Mb genomic segments.

fastsimcoal2 now allows one to estimate demographic parameters from the (joint) site frequency spectrum (SFS) using simulations to compute the expected SFS and a robust method for the maximization of the composite likelihood.

new version of fastsimcoal2 : fsc28 (September 2023)

fsc28 main new feature is the ability to deal with sample spatial and time heterogeneity with the introduction of the notion of sfs pools.

downloads (fsc28)

Windows 64 bits

Linux 64 bits

MacOSX

manual

what's new in fastsimcoal28 (compared to ver 2.7)

New features

New syntax in the .tpl files to deal with sample heterogeneity. We introduce the concept of sfs pools where the sfs of different samples can be computed as a pool. It allows for considering any spatial of temporal heterogeneity. New key word “sfspool” in deme size section
Possibility to record the deme of origin of chromosome segments when implementing an admixture even so that it is possible to simulate chromosome painting. New keyword “recordAdmOrigin” in historical events
New command line options (-y and -z) to fine tune the parameter estimation procedure
Other changes and bug corrections:

When simulating several data files with definition files (.def) the SFSs are written in different files, either in separate directories with the -j option, or in the same directory without the -j option
Program was crashing when simulating exponential growth and migration. Bug found by Jason Weir.
Optimisation of computations when estimating data from multidimensional SFS
Bad computation of lhood when estimated from the maxL.par files as compared to that computed during parameter estimations, in case of population growth. Bug found by Kyle Lewald
Incorrect simulations from par files when some demes are explicitly killed. Bug found by Kyle Lewal

See this page for a complete list of changes since first fastsimcoal release

benchmarks

Comparisons with other coalescent simulations programs such as ms, simcoal2 or MaCS can be found here

getting started

A quick overview of how to get started with fastsimcoal can be found here (but it is better to read the manual first)

additional scripts for the preparation of input files and the analysis of results

A series of R and bash scripts decribed and made available here have been developed by several people from our group to facilitate the analysis of the results of fsc27 as well as for preparing input file

running fsc27 on a mac

I have realized (thanks to Melissa Wilson Sayre) that the plain version of fsc26 and following will not run on mac osX unless you have installed a recent version of gcc.

This is because fsc26 and above is multithreaded and it uses intel's libraries based on openMP, which are not distributed anymore with recent versions of mac OSX.

So to be able to run fsc28 on your mac, you need to first install a recent version of gcc.

To do so, follow e.g. these steps:

Download gcc-10.2-bin.tar.gz
Open a terminal
cd to the download folder
Extract the tar archive with the command
gunzip gcc-10.2-bin.tar.gz
Install gcc ver 5.1 in /usr/local with the command
sudo tar -xvf gcc-10.2-bin.tar -C /.

problems running fsc27 on old versions of linux (kernel too old)

It seems that fsc27 (and more recent versions) is not able to run on old linux version with an old kernel, potentially due to the need of openmp libraries that need to be dynamically linked to the program.

bug reports

Send an email to Laurent Excoffier or use the Google group list

discussion list

A Google group on fastsimcoal (https://groups.google.com/forum/#!forum/fastsimcoal) has been created to promote discussion or allow queries on any aspect of fastsimcoal. Please use it!

citation

fastsimcoal2:

Excoffier, L., Kapopoulou, A., Marchi,, N. (2023) Demogenomic inference from spatially and temporally heterogeneous samples. Molecular Ecology Resources https://doi.org/10.1111/1755-0998.13877

Excoffier, L., Marchi,N., Marques, D. A., Matthey-Doret, R., Gouy, A., Sousa, V. C. (2021) fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics. 37:4882-4885.

Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V.C., and M. Foll (2013) Robust demographic inference from genomic and SNP data. PLOS Genetics, 9(10):e1003905.

fatsimcoal:
Excoffier, L. and Foll, M (2011) fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios Bioinformatics 27: 1332-1334.

Last updated by L. Excoffier on 16..10.2023