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. 2024 Jun 8;6(2):lqae066. doi: 10.1093/nargab/lqae066

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© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://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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Figure 3. — Phenograms highlighting selected clades for two Panther orthogroups: (A) PTHR11818:SF19 (β-crystallin A4); (B) PTHR48043:SF140 (UDP-glucuronosyltransferase, E.C. 2.4.1.17). For each panel, a gap-distance based evolutionary tree and multiple sequence alignment are shown. Each panel also shows the total number of canonical and isoform sequences examined and the number of organisms with a sequence in this orthogroup, followed by a list of proposed replacement (P1) clades and their sizes and costs. In the tree, blue sequences are canonical accessions; the darker sp|P53673|HUMAN --> sequence in panel (A) was selected by the MANE (13) consortium. Accessions shown in red and orange are proposed to be changed; orange canonicals have been selected by MANE. For both red and orange, there is a corresponding green isoform that is proposed to be canonical. Black accessions indicate canonical isoforms that are not included in a low-cost clade. Gray accessions indicate non-canonical isoforms. Numbers after each protein accession indicate the length of the sequence, and its assigned clade (P1). This figure was drawn using the ggtree package for ’R’ (27).