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.

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