To run strappyMcBootClade type the following into a unix interpreter:
python strappyMcBootClade_vxxx.py <popFile.txt>
Where "xxx" refers to the version number. Current version is 1.3.
ASSUMPTIONS:
strappyMcBootClade only considers codons with 2 or fewer changes between them and 2 or fewer alleles at the codon of interest. For codons with 2 changes, pathway with fewest number of nonsynonymous changes is assumed. Sites with missing data are partially ignored by removing that sample from the codon-by-codon analysis. Codons with missing data are assumed to have 0.71875 synonymous sites and 2.28125 nonsynonymous sites. Missing nucleotides should be specified by 'N', missing amino acids will be specified by 'X'.
Citation Information:
Sharbrough et al. Inefficient purifying selection and variation in functional constraint drives accelerated but heterogeneous accumulation of harmful mutations in asexual lineages of a freshwater snail. In review.