In general, we should be trying to rephrase things in terms of general biological notions instead of partis specific terminology, in particular with respect to output data and nesting language. Of particular note, we should be using clonal_family over cluster wherever possible. Can pile on other changes to this issue as we notice them.
This came out of: matsengrp/olmsted#115, and specifically https://github.com/matsengrp/olmsted/commit/55608edfa8765692b6bd6e26b348cbab10616e35#r32606502
In general, we should be trying to rephrase things in terms of general biological notions instead of partis specific terminology, in particular with respect to output data and nesting language. Of particular note, we should be using
clonal_familyoverclusterwherever possible. Can pile on other changes to this issue as we notice them.