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