For an approach that makes use of multiple alignments, our assumption is that a non-negligible amount of the existing RNA RNA interaction contains compensatory changes across the binding sites.
The RNAstrand tool is designed specifically to predict the reading direction of a multiple sequence alignment under the assumption that the alignment contains an evolutionary conserved RNA secondary structure.
In the C-terminal region, in particular, no conserved motif was identified in the alignment, supporting the assumption that this is a relict of the linker sequences of the multi-modular PKS Type I.
As we move through these five schools of thought – which are addressed in a roughly chronological order – we discern an increasing degree of alignment with the assumptions and methods of IMP scholars.
On the other hand, studies that have relied on global alignments have faced extreme alignment problems, making assumptions on true homology difficult or impossible.
To test that assumption, alignments of sequences of individual genes from two pairs of strains from two different clades were bootstrapped and compared with the topology of the tree based on concatenated alignment.
Codeml assumes a time-continuous Markov process of codon evolution [ 27] and ω-ratios were computed as Maximum-Likelihood-Estimates that maximize the probability to observe the multiple alignment under the assumptions specified below as outcome of the Markov process.
Phylogenetic analysis using multiple sequence alignments rests on the assumption that the residues (nucleotides or amino acids) at the same position in every sequence in the alignment are homologous.
Yet on epiphenomenalist assumptions, this alignment could not receive a genuine explanation.
Orlikowski and colleagues posited that degrees of alignment between organisational members' assumptions, expectations, interpretations and understanding of the role of an innovation ultimately determined outcomes following implementation [ 18].
