Options & Examples

After a successful compile, start hitchhiking by typing

./hitchhiking

As a result, the options are listed:

-n <NUM> sample size = NUM
-N <NUM> population size = NUM
-r <NUM> rate of recombination = NUM; 0 <= NUM <= 1
-S <NUM> selectiv advantage of advantageous allele = NUM; 0 <= NUM <= 1; NUM = 0 neutrality
[-t <NUM> scaled mutation parameter = NUM; only for -v 1; NUM >= 0]
[-d <NUM> number of steps simulated in the logistic model = NUM; default NUM = 1000]
[-w <NUM> run Wright Fisher model with NUM iterations; default NUM = 0]
[-y <NUM> run exact Yule model with NUM iterations; default NUM = 0]
[-l <NUM> run logistic model with NUM iterations; default NUM = 0]
[-k <NUM> run starlike model with NUM iterations; default NUM = 0]
[-s <NUM> seed for random number generator = NUM; default: NUM = system clock]
[-v <NUM> verbosity; 0: sweep only, 1: add neutral phase; default NUM = 0]
[-h print this help message]

An example run of hitchhiking might look as follows:

./hitchhiking -n 12 -N 100000 -S 0.01 -r 0.001 -w 1

and generates output similar to

n        12     N     100000   S     0.010  r    0.0010     w    1    \
y        0      l     0        k     0      s    1146268877
Case    cinb    btoB    FSizes
WriF    0       0       8       1       1       1       1

where ' \' indicates continuation of a line. This output has the following structure:

• first line: repeats the parameters used for the simulation;
• second line: is a table header;
• third and last line: reports in tab-delineated format
  1. the type of model simulated;
  2. the number of coalescence events in the wild-type background;
  3. the number of recombination events from the wild-type to the beneficial allele;
  4. the family sizes; the first entry gives the number of lines that trace back to the founder of the sweep, followed by a list of the recombinant families in no fixed order .

More detailed output can be obtained using verbosity level 1. In this case the user should also set a mutation rate; for example

./hitchhiking -n 12 -N 100000 -S 0.01 -r 0.001 -w 1 -t 5 -v 1

might generate

n        12     N     100000   S     0.010  r    0.0010     w    1    \
y        0      l     0        k     0      s    1146269119
Case Spec  C     S     M     K     H     thetaW   thetaPi   tajimasD
WriF  (1.428302,1.013126,0.213380,0.000000,0.001960,0.000000,0.000000,\
0.231102,1.000548,0.000000,0.000000)   (2,1,0,0,0,0,0,1,0,0,0,0)    15\
8   0.513889   4.967089   4.621212   -0.298973

The first two lines of this output are unchanged compared to the first run. The third line lists in tab-delineated format

1. the type of model simulated;
2. a vector of the lengths of the branches leading to 1, 2,..., n tips of the gene tree;
3. a vector of the haplotype counts;
4. the number of segregating sites;
5. the count of the major haplotype in the sample;
6. the number of distinct haplotypes;
7. Watterson's $\theta$;
8. the mean number of pairwise nucleotide differences per site, $\pi$;
9. Tajima's D.