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 sequences 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.   Optionally  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 afterwards (forward in time).

       -ej t i j
              Speciation event at time t. Creates population j from individuals 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