Bruno Vieira | @bmpvieira
Run PSMC across a wide range of social insects and their solitary relatives
Short answer: I don't know!
Long answer: I can try to explain...
Generating the genealogical relationship between k sampled sequences from a population with constant size N and no recombination
Ancestral Recombination Graph (ARG)
Along the chromosome instead of back in time
1. Recombination in ancestral material;
2. Recombination in non-ancestral material that has ancestral material to both sides;
3. Recombination in non-ancestral material that has ancestral material only to the left;
4. Recombination in non-ancestral material that has ancestral material only to the right;
5. Recombination in an individual that carries no ancestral material.
Spatial approach by Wiuf and Hein, 1999
1. Recombination in ancestral material;
2. Recombination in non-ancestral material that has ancestral material to both sides;
3. Recombination in non-ancestral material that has ancestral material only to the left;
4. Recombination in non-ancestral material that has ancestral material only to the right;
5. Recombination in an individual that carries no ancestral material.
"New coalescent-based method that can efficiently infer population size changes from multiple genomes, providing access to a new store of information about the recent past."
http://simons.berkeley.edu/sites/default/files/docs/1213/slidesmailund.pdf
http://simons.berkeley.edu/sites/default/files/docs/1213/slidesmailund.pdf
http://simons.berkeley.edu/sites/default/files/docs/1213/slidesmailund.pdf
$ git clone https://github.com/lh3/psmc.git
$ cd psmc
$ make
$ cd utils
$ make
Usage: psmc [options] input.txt
Options: -p STR pattern of parameters [4+5*3+4]
-t FLOAT maximum 2N0 coalescent time [15]
-N INT maximum number of iterations [30]
-r FLOAT initial theta/rho ratio [4]
-c FILE CpG counts generated by cntcpg [null]
-o FILE output file [stdout]
-i FILE input parameter file [null]
-T FLOAT initial divergence time; -1 to disable [-1]
-b bootstrap (input be preprocessed with split_psmcfa)
-S simulate sequence
-d perform decoding
-D print full posterior probabilities
Usage: psmc_plot.pl [options] <out.prefix> <in.psmc>
Options: -u FLOAT absolute mutation rate per nucleotide [2.5e-08]
-s INT skip used in data preparation [100]
-X FLOAT maximum generations, 0 for auto [0]
-x FLOAT minimum generations, 0 for auto [10000]
-Y FLOAT maximum popsize, 0 for auto [0]
-m INT minimum number of iteration [5]
-n INT take n-th iteration (suppress GOF) [20]
-M titles multiline mode [null]
-f STR font for title, labels and tics [Helvetica,16]
-g INT number of years per generation [25]
-w INT line width [4]
-P STR position of the keys [right top]
-T STR figure title [null]
-N FLOAT false negative rate [0]
-S no scaling
-L show the last bin
-p convert to PDF (with epstopdf)
-R do not remove temporary files
-G plot grid
Bruno Vieira | @bmpvieira
Yannick Wurm | @yannick__
© 2014 Bruno Vieira CC-BY 4.0