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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
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Source code for SimBac, a bacterial genome simulator
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