The Square interface on the iPhone, for example, had the same alignment of form, and same organization since the very beginning.
The rationale for the merger is the same: alignment of goals, communities and day-to-day activities, but very little overlap between programs and funding sources.
In the analysis, the new sequences were compared with consensus sequences (50% threshold) representing the HIV-1 variants from the same alignment used for phylogenetic tree analysis.
In our paper, we applied the modified branch-site model A of [ 45] in two consecutive tests (test1 and test2 in [ 46]) to the same alignment used for the site-based models, but we could not detected the positive selection site.
However, we have previously demonstrated that MAQ is inadequate for the analysis of pooled DNA samples [ 9], and wanted to use the same alignment tool for both the individual and pooled sample to minimize differences in variant calling due to variable alignments.
Multiple alignments were created in CLUSTALX [ 67] and trimmed with Jalview [ 68], and the same alignment was used for analysis by neighbor joining (NJ) and maximum parsimony (MP).
Two alternative trees, using RAxML [ 45] and Treefinder [ 39], were constructed from the same alignment as used for the tree shown in Figure 2A.
Multiple alignments were created in CLUSTALX (Thompson et al. 1997), manually adjusted, and visualized with Jalview (Waterhouse et al. 2009), and the same alignment was used for analysis by neighbor joining or maximum parsimony.
The same alignment file produced for the contig coverage calculations was parsed using an in-house script to obtain the proportion of the original genome's length covered by the longest aligning contig (maximum contig coverage).
Validation studies used Segments 3 (3,633,818 - 3,658,818) and 4 (4,754,067 - 4,779,067), and the same alignment techniques used for Segments 1 and 2. Primers were designed to amplify ~500 bp overlapping segments of the genome in Segments 1 and 2 in eight ECOR strains (Additional File 1, Table S1).
