v2.1.0

First and long overdue Turing-centered release.

Whale v0.3

Implemented a delayed-acceptance step, (using the simple factorization of the posterior as prior times likelihood). This will be the last v0.x version normally, as a substantially improved version is in development (see dev and pgm branches).

Whale v0.2

Whale library with methods for ML and Bayesian inference under the DL + WGD model. Allows estimation of (branch-specific) duplication and loss rates as well as WGD retention rates for a given species tree based on a set of (posterior distributions of) gene trees. This allows statistical testing of WGD hypotheses. Version 0.2 extends version 0.1 (described in Zwaenepoel & Van de Peer (2019) https://doi.org/10.1093/molbev/msz088) with consensus reconciled trees as well as subgenome ambiguity (which allows probabilistic subgenome assignment for allopolyploids).