| filter.allele_ages | Filter allele_ages by quality of tree |
| get.allele_ages | Compile allele ages file |
| get_hap_matrix | Get haplotype matrix (L x N) |
| PolyTest | Test for evidence of polygenic selection |
| PolyTest_Init | Initialise polygenic selection test |
| PolyTest_ResampleSNPs | Resample selection p-values |
| read.avg_rate | Parse average rate file |
| read.coal | Parse coal file |
| read.freq | Parse freq file |
| read.haps | Parse haps file |
| read.lin | Parse lin file |
| read.mut | Parse mut file |
| read.qual | Parse qual file |
| read.sample | Parse sample file |
| read.sele | Parse sele file |
| relater | relater |
| timesTwo | Multiply a number by two |
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