scrm - An accurate coalescent simulator for genome-scale
sequences
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]
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.
- -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.
- -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.
- -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.
- -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).
- scrm 4 1 -t 10 -r 4 10000
- scrm 4 1 -t 10 -r 4000 100000000 -l 0
- scrm 4 1 -t 10 -r 4000 100000000 -l 300000