SimBac README

SimBac uses the GNU Scientific Library, which can be installed on Linux Ubuntu by running:
sudo apt-get install gsl-bin libgsl0-dev libgsl0ldbl

On a Mac, the GNU Scientific Library can be install via Homebrew, running:
brew install gsl

On Windows, the GNU Scientific library can be obtained through a Cygwin add-on.

To compile SimBac, change to the directory with the source files and run:

g++ *.cpp -lgsl -lgslcblas -lm -O2 -o SimBac

To view the options to be passed to SimBac, run without any arguments or with the "-h" flag:

./SimBac
./SimBac -h

    -N NUM Sets the number of isolates (default is 100)
    -T NUM Sets the value of θ, the site-specific mutation rate, between 0 and 1 (default is 0.01)
    -m NUM Sets the lower bound of site-mutation (divergence) in a region of external recombination, between 0 and 1 (default is 0)
    -M NUM Sets the upper bound of site-mutation (divergence) in a region of external recombination, between 0 and 1 (default is 0)
    -R NUM Sets the site-specific rate of internal (within species) recombination, R_i (default is 0.01)
    -r NUM Sets the site-specific rate of external (between species) recombination, R_e (default is 0)
    -D NUM Sets the average length of an internal recombinant interval, δ_i (default is 500)
    -e NUM Sets the average length of an external recombinant interval, δ_e (default is 500)
    -B NUM,. . .,NUM Sets the number and lengths of fragments of genetic material (default is 10000)
    -G NUM,. . .,NUM Sets the size of gaps between each fragment, must be the same number of gaps as there are numbers of genetic fragments (default is 0,. . .,0)
    -s NUM Use given seed to initiate random number generation
    -o FILE Name of file to write generated sequences (FASTA format)
    -c FILE Name of file to write clonal genealogy (Newick format)
    -l FILE Name of file to write local trees (Newick format)
    -b FILE Write log file of internal recombinant interval locations
    -f FILE Write log file of external recombinant interval locations
    -g FILE Name of file to write log of recombination break points and origins and recipient lineages of the recombinant material (Only recommended for small ARGs)
    -d FILE Name of file to export ancestral recombination graph (DOT file)
    -a Include ancestral material in the DOT graph


For example, to simulate a population of 100 isolates with genome length 1Mbp and R=0.01, θ=0.01 run:

./SimBac -N 100 -B 1000000 -R 0.01 -T 0.01 -o genomes.fasta -c clonal_frame.nwk

Linear genomes can be approximated by placing a large gap at the end of the ancestral block. For example, to simulate a linear genome of length 100kbp, run:

./SimBac -N 100 -B 100000 -G 1000000 -o genomes.fasta -c clonal_frame.nwk

This places a gap of length 1Mbp after the genome, meaning recombinant intervals cannot include both the first and last element of the genome.


Supplemantary information with a manual and technical description can be found here:
https://github.com/tbrown91/SimBac/blob/master/SimBac_supp.pdf