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SCRM(1) General Commands Manual SCRM(1) NAME scrm - An accurate coalescent simulator for genome-scale sequences SYNOPSIS scrm nsamp nloci [-hvL] [-r rec L [-l l] [-sr b rec]... ] [-I npop s1 ... sn [M] [-eI t s1 ... sn [M]]... [-M M] [-eM t M]... [-m i j M] [-em t i j M]... [-ma M11 M21 ... Mnn] [-ema t M11 M21 ... Mnn]... [-es t i p]... [-ej t i j]...] [-n i n] [-en t i n]... [-eN t i n]... [-g i a] [-eg t i a]... [-G t a] [-eG t a]... [-t theta [-oSFS] [-st b theta]... ] [-seed seed [seed2 seed3]] [-p digits] DESCRIPTION scrm is a coalescent simulator for biological sequences. Different to similar programs, it can approximate the Ancestral Recombination Graph with arbitrary precision. This allows you to rapidly simulate long se- quences with essentially correct genetic linkage between sites. OPTIONS Recombination: -r R L Set recombination rate to R and locus length to L. -sr p R Change the recombination rate R at sequence position p. -l l Set the approximation window length to l. Population Structure: -I npop s1 ... sn [M] Use an island model with npop populations, where s1 to sn individuals are sampled each population. Option- ally assume a symmetric migration rate of M. -eI t s1 ... sn [M] Sample s1 to sn indiviuals from their corresponding populations at time t. -M M Assume a symmetric migration rate of M/(npop-1). -eM t M Change the symmetric migration rate to M/(npop-1) at time t. -m i j M Set the migration rate from population j to population i to M -em t i j M Set the migration rate from population j to population i to M at time t. -ma M11 M21 ... Sets the (backwards) migration matrix. -ema t M11 M21 ... Changes the migration matrix at time t -es t i p Population admixture. Replaces a fraction of 1-p of population i with individuals a from population npop + 1 which is ignored af- terwards (forward in time). -ej t i j Speciation event at time t. Creates population j from individu- als of population i. Population Size Changes: -n i n Set the present day size of population i to n*N0. -en t i n Change the size of population i to n*N0 at time t. -eN t n Set the present day size of all populations to n*N0. -g i a Set the exponential growth rate of population i to a. -eg t i a Change the exponential growth rate of population i to a at time t. -G a Set the exponential growth rate of all populations to a. -eG t a Change the exponential growth rate of all populations to a at time t. Summary Statistics: -t THETA Set the mutation rate to THETA = 4N_0u, where u is the neutral mutation rate per locus. -T Print the local genealogies in newick format. -O Print the local genealogies in the Oriented Forest format. -L Print the TMRCA and the local tree length for each segment. -oSFS Print the site frequency spectrum. Requires to set the mutation rate. -SC [ms|rel|abs] Scaling of sequence positions. Either relative to the locus length between 0 and 1 (rel), absolute in base pairs (abs) or ms-like (ms). Other: -seed SEED [SEED2 SEED3] The random seed to use. Takes up three integer numbers. -v, --version Prints the version of scrm. -h, --help Prints this text. -p digits Number of significant digits used in output. Examples Five independent sites for 10 individuals using Kingman's Coalescent: scrm 10 5 -t 10 A sequence of 10kb from 4 individuals under the exact ARG: scrm 4 1 -t 10 -r 4 10000 A sequence of 100Mb using the SMC' approximation: scrm 4 1 -t 10 -r 4000 100000000 -l 0 Same as above, but with essentially correct linkage: scrm 4 1 -t 10 -r 4000 100000000 -l 300000 Version 1.7.2 April 2016 SCRM(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | Examples
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