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. 2014 Nov 18;6(12):3199–3209. doi: 10.1093/gbe/evu252

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© The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 5.— — Phylogenetic trees reconstructed using the most reliable indels characters coded from MSAs produced by (A) PRANK, (B) MAFFT, and (C) CLUSTALW and filtered by the RELINDEL method. The correct primate phylogeny was reconstructed when using indels derived from both PRANK and MAFFT. Homo is misplaced in the tree reconstructed based on CLUSTALW MSAs (the erroneous branch is marked in red). Additional statistical information is provided in panel (D) (Informative, number of informative characters; CI, consistence index; RI, retention index).