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Whereas the cladogram in Fig. 1 is based on alignment of proteins, we used gene names for clarity.
Site numbering is based on alignment against bovine RH1 opsin (rhodopsin).
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AIBIMM is based on alignment-independent classification in a coordinate system, while RDP-II uses a predefined model for classification.
The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation.
Combining these approaches should reveal whether clade support is based on alignment-ambiguous regions, and, if so, whether it is dependent on how these regions are aligned.
In GAML, we filter PacBio reads by a completely different approach, which is based on alignments, rather than k-mers.
Phylogenetic analysis from MEP/carotenoid enzymes pathways was based on alignment of concatenated sequences from 29 plant species and one moss species.
The ancestral allele was based on alignment to the chimpanzee sequence.
The first method was based on alignment and assembly using reference genomes from two strains within the subspecies tularensis type A1, FSC198 [7] and SCHU S4 [9].
They claim the conclusions reached in [ 12] are based on alignment artifacts.
Proposed 5' start of RNAs was based on alignment with known 5' start sites of homologous RNAs.
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