Phylogenetic analyses were performed based on THV P1, 2C/3C/3D, and full polyprotein sequence excluding divergent aa 799 1199.
Within this overall diversity, orthologs sequence identities are highly conserved, with average pairwise distances among orthologs less than 0.011 for the major α1 and β1 isoforms, and less than 0.140 for the α2, β2 (excluding divergent duplication products), β3, and β4 minor isoforms.
Consequently, we checked the items for compliance with the Rasch model and excluded divergent items.
A divergent transcript was only included if (1) >10% of the transcript overlapped the proximal region of a promoter (± 500 bp relative to the TSS) driving expression of a primary transcript >1 kb in size on the opposite strand and (2) the transcript was <50% the size of the primary transcript, which effectively excluded divergent enhancer-transcript pairs.
Because this approach excludes divergent regions, we calculated OHR with an alternative and more inclusive approach (OHRORF) as the ratio of the transcript's longest ORF (in the BLASTx-defined reading frame) relative to the length of its corresponding N. vectensis protein.
Divergent bit scores were re-evaluated by comparing them to other fungal vs. animal/plant scores to exclude divergences only proper to the two fungi initially considered.
The RMS error curves in Figure 6 were computed from the estimation errors recorded in each of the 100 Monte Carlo trials, excluding the divergent realizations.
He tabulated the frequency distributions of glyphs in ten texts (excluding the divergent Santiago Staff) and found that they coincided with the distribution of syllables in ten archaic Rapanui texts such as the Apai recitation, with nearly identical deviations from an ideal Zipfian distribution.
Nonetheless, to avoid erroneously excluding highly divergent sequences, the nearest blastp matches to human Set8 were included in our analyses.
This remained the case also after excluding highly divergent sites such as Malindi, MMP 1, ZE 1 and ZW 2 (R2 = 0.0015; p = 0.248).
The phylogenetic analysis was conducted using NJ, ML and bayesian algorithms, excluding highly divergent sequences as well as heavily truncated ones but retaining representatives of ecdysozoans, lophotrochozoans and of the major chordate taxa (see Additional file 2).
