- Section S.2 of the Supplement states that "The fraction of
trials whose maximum parsimony score is less than that of the of the
original dataset is the empiricial p-value". The phrase "less than"
should read "less than or equal to".
- The version of xscape used in the paper had a bug that
allowed a parasite/gene node p on a host/species edge h to switch one
of its children to the same host edge h. This effectively becomes a
duplication. In regions of the cost landscape where switches are less
expensive than duplications, xscape would choose these switches over
duplications. This bug has been corrected in version 0.0.4 of xscape.
- Version 0.0.4 had a bug that caused xscape to swap transfer and loss costs when the ranges of these two costs were not the same. This has been corrected in version 0.0.5 of xscape.