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 ([email protected]) 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