Aphid
This is the technical documentation
for the aphid method:
distinguishing gene flow from incomplete lineage sorting,
and the associated command-line program:
- The original paper describing the method: https://doi.org/10.24072/pcjournal.359.
- The associated program to use the method: https://codeberg.org/isem/aphid.
This document assumes that you are familiar with the method described in the paper. Readers interested in the context, the intuition, or the meaning of the method are encouraged to refer to the original paper instead, as these are not covered here.
This document explains how to install the aphid program
and how to use it.
It also specifies the detail of expected inputs,
of the calculation performed by the program
and the outputs produced.
Bug reports, feature requests and contributions are welcome here.