rrnni - Manipulate with RNNI Tree Space
Calculate RNNI distance between and manipulate with ranked
trees. RNNI stands for Ranked Nearest Neighbour Interchange and
is an extension of the classical NNI space (space of trees
created by the NNI moves) to ranked trees, where internal nodes
are ordered according to their heights (usually assumed to be
times). The RNNI distance takes the tree topology into account,
as standard NNI does, but also penalizes changes in the order
of internal nodes, i.e. changes in the order of times of
evolutionary events. For more information about the RNNI space
see: Gavryushkin et al. (2018) <doi:10.1007/s00285-017-1167-9>,
Collienne & Gavryushkin (2021)
<doi:10.1007/s00285-021-01567-5>, Collienne et al. (2021)
<doi:10.1007/s00285-021-01685-0>, and Collienne (2021)
<http://hdl.handle.net/10523/12606>.
