In vitro methods, such as the re-sequencing of targeted amplicons, are generally more appropriate when sequence data is limited or when one is interested in polymorphisms in specific genotypes or candidate genes.
Divergences were estimated under a Yule speciation process that is generally more appropriate when considering sequences from different species [ 36].
The conclusions remain unchanged; yet, we think that, for future evaluation of TM helix properties, sequence complexity computations that are unaffected by variations just among the aliphatic hydrophobic residues are more appropriate since, then, the sequence complexity criterion becomes more orthogonal relative to hydrophobicity.
Because these methods are more appropriate for the high sequence divergences, they could provide an important cross-check of the codon-based results and confirmed that the GA oxidases underwent functional divergence.
We characterized almost all miRNAs newly described in the original paper (Ruby, Stark, et al. 2007), with the exception of 18 sequences that did not pass our strict filtering procedure (which is more appropriate for our larger sequencing data set).
It could be presented in a more appropriate manner showing the nucleotide sequence (together with the amino acid sequence) so that the reader can understand why the data supports ribosome slippage, and exactly which frame the ribosomes are in with the different constructs.
We have focused primarily on the relationships supported by distance analysis, since this methodology is more appropriate for highly divergent sequences.
Typically, each algorithm is more appropriate for a specific type of sequencing technology, target sequence, organism, and experimental condition.
Therefore, it is noteworthy that inclusion of intron sequences seems more appropriate for the phylogenetic reconstruction at lower taxonomic levels.
