Regarding the general differences in bootstrap and PP values, the different software packages used and the difference in the data set (taxon sampling, alignment and included sites) may have contributed to the higher support found for several clades.
Of 194,384 sites included in the analysis, 13,776 sites could unambiguously be characterized as having DAs in the European population, including sites fixed for the DA, giving an overall frequency of 0.07 per site in the alignment (and including those fixed for the ancestral allele, i.e., invariant sites with 0 DAs; note only sites with no missing data were analyzed).
Bowtie267 (v2.2.4) was then used to align reads to reference genomes using the default, paired-end alignment options and including the singleton reads.
For genes that displayed alternative splicing patterns, the presumed ancestral isoform sequence was identified through alignment methods and included in the dataset while the alternative isoforms were not.
This threshold also corresponds to 0.26%% of all nrESS alignments (81,520 of 31,756,465) and includes 7907 out of 7970 nrESS.
Importantly, the human sequence was removed from the alignment and not included in either the neutral rate estimation or the site-specific "observed" estimates, and therefore it is not included in the RS score.
Where the same residue was present more than once in the same position in the alignment, it was considered significant due to the diversity of the alignment and was included in the consensus.
Pairwise matches that are present in the LIS chain for both the reference and query sequences (delta-filter -1) are saved for use in the multiple alignment and can include inversions.
Results are hyperlinked to the external databases, and include alignment descriptions and details about the pairwise alignments of each contig with the corresponding BLAST hits.
(102) The images are usually aligned starting from low tilt angles, and the alignment progressively includes higher tilts.
A 71-taxon, 1265-site atp1 alignment was similarly constructed and included the same gymnosperm outgroup genera as above, 24 monosulcates, 32 nonparasitic eudicots and 12 Rafflesiales.
