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source_code_yeaman_PNAS_2013.tar (1.3 MB)
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| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| source_code_yeaman_PNAS_2013.tar | 2013-04-17 | 1.3 MB | |
| init_file.txt | 2013-04-17 | 4.2 kB | |
| README.txt | 2013-04-17 | 2.1 kB | |
| Totals: 3 Items | 1.3 MB | 0 |
This archive contains the source code to compile the heavily modified version of Nemo that I used to run the simulations in the paper "Genomic rearrangements and the evolution of clusters of locally adaptive loci". The simulations have rather dirty coding style, so please excuse the use of global variables and such; I sometimes got excited about the results and was more eager to get code running than write it beautifully. I have tried to include comments to explain some of the code; if you have questions or would like any aspect of it clarified (or you find a bug), please don't hesitate to contact me. The Makefile included here will require some modifications to work on your computer (specifying the GSL pathway, etc.). I have also included a sample init file, showing how the variables are specified. Comments are included to clarify the meaning of each parameter. The files that I used to record the state of each locus (.qfreqall0 and .qfreqall1) have the following format, with .qfreqall0 and .qfreqall1 representing the state of the populations in patch 0 and 1, respectively: generation mode mean locus FST mode_code 1 500 -0.05 1992 0 0.979116 0 500 -0.05 1991 1 0.97124 0 500 0 1989 2 0.972205 0 500 0 1992 3 0.984064 0 500 0 1988 4 0.978122 0 500 0 1987 5 0.964348 0 . . . The columns are indicated by the headings (the second line is meaningless in this version). For the PNAS paper, I did not use the "mean" or "FST" column, so I haven't checked whether they have bugs in this version. The columns have the following interpretation: -generation: this indicates the generation at which the population census was conducted. -mode: this indicates the effect size of the allele that was most common in the patch. -locus: this indicates the number of the locus (from 0 to X). One locus per line. -mode_code: this indicates whether the locus was neutral (code == 0) or selected (code > 0). In the latter case, the codes were initialized from 1:10 in the beginning of the simulations and these codes were used to track the copy number of each locus.