The optical map results describe two categories of global alignments, either 'restrictive' (level 1) or 'permissive' (level 2), and one category of local alignment (level 3).
Many features of individual alignments are useful for sampling homologous sequences (e.g., alignment coverage, level of similarity, etc) but their organization and accessibility across the BLAST result page do not facilitate their interpretation.
Subsequent to alignment, the level of similarity among the coding sequences (cds) of different genes ranged from 53.1% to 97.7% and from 95%to99.8%8% for the different alleles within a gene.
However, the 'strict' conditions (default parameters in Gblocks) are indeed very stringent (e.g. no character was selected in ≈40% of the multiple sequence alignments with level of divergence ×3), and phylogenetic trees inferred from the remaining blocks (when these existed) were always less accurate than those inferred from the blocks returned by the 'relaxed' conditions (results not shown).
Despite these institutionalized alignment efforts, we observed difficulties that could be attributed to lack of alignment at the level of the research project.
This is in alignment with the level of ATP during these phases.
We built a multiple alignment at the level of single repeats to define the EPTP repeat consensus sequence (Figure 5).
In other words, there appears to be a somewhat deterministic relationship between the number of gaps in an alignment and the level of phylogenetic accuracy one can expect in an NJ analysis.
It must, however, be noted that the actual relationship between the percentage of gaps in an alignment and the level of phylogenetic accuracy that can be expected is vastly different between the two gap treatment methods, MD and BC.
To visualize the alignment results at the level of individual proteins, the output alignments from the dotplot were collected, and for each alignment, the aa positions of the alignment and Ups category of the pair of proteins were determined.
