Data from: Generalized bootstrap supports for phylogenetic analyses of protein sequences incorporating alignment uncertainty

Maria Chatzou, Evan Wade Floden, Paolo Di Tommaso, Olivier Gascuel & Cedric Notredame
Phylogenetic reconstructions are essential in genomics data analyses and depend on accurate multiple sequence alignment (MSA) models. We show that all currently available large-scale progressive multiple alignment methods are numerically unstable when dealing with amino-acid sequences. They produce significantly different output when changing sequence input order. We used the HOMFAM protein sequences dataset to show that on datasets larger than 100 sequences, this instability affects on average 21.5% of the aligned residues. The resulting Maximum...
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