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. 2018 May 14;34(21):3646–3652. doi: 10.1093/bioinformatics/bty389

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© The Author(s) 2018. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 2. — A. Representation of the <branchingOut> tag. B. Representation of the <transferBack> tag. C. Representation of a <branchingOut> tag followed by a <loss> tag. D. Representation of the <bifurcationOut> tag. These figure uses the same conventions as Figure 1 with the following additions. For the <bifurcationOut> tag (D.), which is specific of the model of Szöllősi et al. (2013b), extinct/unsampled lineages are represented as branches of the species tree that do not extend all the way to the right. Diamonds and triangles respectively represent a transfer leaving and entering a branch of the species tree (note that the transfers leave a branch of the species tree that corresponds to an extinct/unsampled lineage)