These limitations involve the data source, i.e. detection of segmental duplications and reliability of DNA sequence alignments, the approach for inference of mutational events, and the sample effect.
The fast-pace keeps you moving, but the attention to proper alignment, the holistic approach to stretching, resting and a final quiet (savasana) reminded me of how much I loved yoga, and how part of me, now that I'm in this wonderful place, wants to return.
After adjusting for age, sex, diagnosis, cement mantle quality, and stem alignment, the surgical approach remained significant (OR = 2.5, 95% CI: 1.4 4.6; p = 0.002).
Among the various algorithms for aligning multiple sequences, we selected the alignment approach implemented in the PRANK program [16].
The reproducibility of the alignment approach was tested by performing the mapping step with BWA, an alternative alignment program [ 45].
Additionally, some recent molecular analyses recovered the same sister group to the Aculeata as in this study, but the results were sensitive to the alignment approach (Heraty et al. 2011; Klopfstein et al. 2013).
In order to align our RDIP-seq reads to the rDNA repeating unit, we used the alignment approach of Zentner and colleagues [ 55].
As our analyses confirm the studies of other authors that branch support values for some clades are highly dependent on the alignment approach used, we conclude that more attention should be given to alignment construction in phylogenetic analyses in general.
Accordingly, policies that curb the influence of individual donors would be valid under the alignment approach.
Although we have focused on DNA sequence alignments in this study, the approach we describe can also be applied to amino acid alignments.
