Mutation-calling

Mutation-accumulation (MA) experiments followed by whole-genome sequencing (WGS) are considered an approximately unbiased method for mutation determination, as this approach allows all but lethal mutations to accumulate (Ref).

This pipeline was contributed by Ying Sun (fuhuisuen@gmail.com) to perform mutation calling using the data from MA/WGS.

Ref: Eyre-Walker A, Keightley PD. (2007). The distribution of fitness effects of new mutations. Nat Rev Genet 8:610–618

Relationship analysis

1. After the mutation calling, some genes showing excess base-substitution mutations can be identified using bootstrap_check_mut_hotspots.py, which is contributed by Liao Tianhua
2. Ne estimation from the Pies of panmictic population
3. Linear regression between Ne and mutation rate µ, µ and genome size (GnmSize), GnmSize and Ne