These results are provided in a tabular view: the columns headers of the table are ID of the gene candidates, links towards fasta format alignment and divergence profile, alignment length, GC content, introns number and functional annotation of the candidate.
Each panel in figure 4 represents a different MSAM and shows the relationship between MSA error, characterized by average MSA distance from the true alignment, and divergence estimate error, taken to be the average sum of errors across individual branches in the phylogenetic tree for amino acid sequences and nucleotide sequences.
JAS designed this study, sequenced BACs, annotated BACs, designed primers for mapping of BACs, performed sequence alignments and divergence estimates, carried out all of the batch sequence assemblies and quantification of those assemblies and drafted the manuscript.
The distribution of alignment depth and divergence in this training set allows empirical thresholds to be determined.
Consistent with previous studies [ 1- 4, 7, 8], we define significant alignment depth and divergence scores as those that are greater than 3 standard deviations from the mean.
Pairwise differences were used to calculate the nucleotide substitution rate by dividing by the length of the alignment and the divergence dates calculated with histone H3D alignments (González-Orozco et al. 2012; Sherman-Broyles et al. 2014).
Our estimates have been obtained on X and Y regions that include nonhomologous sequences (i.e., DNA repeats and other inserted/deleted sequences), which decreases the quality of the global alignment and increases divergence.
In addition, the evolutionary distance between the two galliforms, chicken and turkey, is considerably shorter than that between chicken and zebra finch, which should facilitate alignment and make divergence estimates more accurate.
Although previous studies showed that atpF- atpH as a barcoding marker was inferior to psbK- psbI, trnH- psbA and matK based on distantly related species [ 5, 8, 9], our data suggested that it was the most promising barcoding marker for duckweeds with respect to high PCR amplification, ease of alignment, and sufficient sequence divergence (Table 1, 2, 3, 4 and Figure 2).
CRT carried out DNA extraction, amplification, alignment, performed all phylogenetic and divergence time analysis, and drafted the manuscript.
Furthermore, the concept offers a much larger operating window regarding beam alignment, divergence and steering and it avoids creating accelerated secondary electrons.
