.TH SCRM 1 "April 2016" "Version 1.7.2" 
.SH NAME
scrm \- An accurate coalescent simulator for genome-scale sequences

.SH SYNOPSIS
.B scrm
.I nsamp nloci
[\fB\-hvL\fR]
[\fB\-r\fR \fIrec L\fR [\fB\-l\fR \fIl\fR] [\fB\-sr\fR \fIb rec\fR]... ]
[\fB\-I\fR \fInpop s1 \fR... \fIsn \fR[\fIM\fR]
[\fB\-eI\fR \fIt s1 \fR... \fIsn\fR \fR[\fIM\fR]]... 
[\fB\-M\fR \fIM\fR]
[\fB\-eM\fR \fIt M\fR]...
[\fB\-m\fR \fIi j M\fR]
[\fB\-em\fR \fIt i j M\fR]...
[\fB\-ma\fR \fIM11 M21 ... Mnn\fR]
[\fB\-ema\fR \fIt M11 M21 ... Mnn\fR]...
[\fB\-es\fR \fIt i p\fR]...
[\fB\-ej\fR \fIt i j\fR]...]
[\fB\-n\fR \fIi n\fR]
[\fB\-en\fR \fIt i n\fR]...
[\fB\-eN\fR \fIt i n\fR]...
[\fB\-g\fR \fIi a\fR]
[\fB\-eg\fR \fIt i a\fR]...
[\fB\-G\fR \fIt a\fR]
[\fB\-eG\fR \fIt a\fR]...
[\fB\-t\fR \fItheta\fR [\fB\-oSFS\fR] [\fB\-st\fR \fIb theta\fR]... ]
[\fB\-seed\fR \fIseed \fR[\fIseed2 seed3\fR]]
[\fB\-p\fR \fIdigits\fR]

.SH DESCRIPTION
.B 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.

.SH OPTIONS
.SS "Recombination:"
.TP
\fB\-r\fR \fIR\fR \fIL\fR
Set recombination rate to R and locus length to L.
.TP
\fB\-sr\fR \fIp\fR \fIR\fR
Change the recombination rate R at sequence position p.
.TP
\fB\-l\fR \fIl\fR
Set the approximation window length to l.
.SS "Population Structure:"
.TP
\fB\-I\fR \fInpop\fR \fIs1\fR ... \fIsn\fR [\fIM\fR]
Use an island model with npop populations,
.IP
where s1 to sn individuals are sampled each population.
Optionally assume a symmetric migration rate of M.
.TP
\fB\-eI\fR \fIt\fR \fIs1\fR ... \fIsn\fR [\fIM\fR]
Sample s1 to sn indiviuals from their
.IP
corresponding populations at time t.
.TP
\fB\-M\fR \fIM\fR
Assume a symmetric migration rate of M/(npop\-1).
.TP
\fB\-eM\fR \fIt\fR \fIM\fR
Change the symmetric migration rate to M/(npop\-1) at time t.
.TP
\fB\-m\fR \fIi\fR \fIj\fR \fIM\fR
Set the migration rate from population j to population i to M
.TP
\fB\-em\fR \fIt\fR \fIi\fR \fIj\fR \fIM\fR
Set the migration rate from population j to
.IP
population i to M at time t.
.TP
\fB\-ma\fR \fIM11\fR \fIM21\fR ...
Sets the (backwards) migration matrix.
.TP
\fB\-ema\fR \fIt\fR \fIM11\fR \fIM21\fR ...
Changes the migration matrix at time t
.TP
\fB\-es\fR \fIt\fR \fIi\fR \fIp\fR
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).
.TP
\fB\-ej\fR \fIt\fR \fIi\fR \fIj\fR
Speciation event at time t. Creates population j
from individuals of population i.
.SS "Population Size Changes:"
.TP
\fB\-n\fR \fIi\fR \fIn\fR
Set the present day size of population i to n*N0.
.TP
\fB\-en\fR \fIt\fR \fIi\fR \fIn\fR
Change the size of population i to n*N0 at time t.
.TP
\fB\-eN\fR \fIt\fR \fIn\fR
Set the present day size of all populations to n*N0.
.TP
\fB\-g\fR \fIi\fR \fIa\fR
Set the exponential growth rate of population i to a.
.TP
\fB\-eg\fR \fIt\fR \fIi\fR \fIa\fR
Change the exponential growth rate of population i to a
at time t.
.TP
\fB\-G\fR \fIa\fR
Set the exponential growth rate of all populations to a.
.TP
\fB\-eG\fR \fIt\fR \fIa\fR
Change the exponential growth rate of all populations to a
at time t.
.SS "Summary Statistics:"
.TP
\fB\-t\fR \fITHETA\fR  
Set the mutation rate to THETA = 4N_0u, where u is the
neutral mutation rate per locus.
.TP
\fB\-T\fR
Print the local genealogies in newick format.
.TP
\fB\-O\fR
Print the local genealogies in the Oriented Forest format.
.TP
\fB\-L\fR
Print the TMRCA and the local tree length for each segment.
.TP
\fB\-oSFS\fR
Print the site frequency spectrum. Requires to set the mutation rate.
.TP
\fB\-SC\fR \fI[ms|rel|abs]\fR 
Scaling of sequence positions. Either relative to the locus
length between 0 and 1 (rel), absolute in base pairs (abs) or ms-like (ms).
.SS "Other:"
.TP
\fB\-seed\fR \fISEED\fR [\fISEED2\fR \fISEED3\fR]
The random seed to use. Takes up three integer numbers.
.TP
\fB\-v\fR, \fB\-\-version\fR
Prints the version of scrm.
.TP
\fB\-h\fR, \fB\-\-help\fR
Prints this text.
.PP
.TP
\fB\-p\fR \fIdigits\fR
Number of significant digits used in output.

.SH Examples
.SS Five independent sites for 10 individuals using Kingman's Coalescent:
.IP
scrm 10 5 \fB\-t\fR 10
.SS "A sequence of 10kb from 4 individuals under the exact ARG:"
.IP
scrm 4 1 \fB\-t\fR 10 \fB\-r\fR 4 10000
.SS "A sequence of 100Mb using the SMC' approximation:"
.IP
scrm 4 1 \fB\-t\fR 10 \fB\-r\fR 4000 100000000 \fB\-l\fR 0
.SS "Same as above, but with essentially correct linkage:"
.IP
scrm 4 1 \fB\-t\fR 10 \fB\-r\fR 4000 100000000 \fB\-l\fR 300000