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Our results represent further evidence that the ITS2 data can be aligned for a taxonomically broad set of organisms and that the alignment yields corroborated alliances of chlorophytan taxa.
A pattern of highly variable positions, nested within conserved, slowly substituting sites across the alignment, yields a valuable resource for studying phylogenetic relationships of both recent and ancient splits [ 1- 4].
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The alignment yielded a tree with poor resolution around the five protein kinases (see Additional file 2 : Figure S9).
We showed that quality trimming and adapter removal improves the alignment yield and mapping speed, both for Tophat and Star.
Also, the quality trimming improves the alignment yield, not only in relative terms but in absolute terms as well (see Additional file 3), and the mapping speed.
Gene families were defined as groups of genes for which the alignments yielded ≥ 90% identity and the alignment length was at least 50% of both the query and matched sequences.
The DaliLite alignment yields a root mean square deviation of 2.4 Å over the backbone atoms of the 28 aligned residues, indicating that the two toxins are indeed structural homologs.
Alignments were evaluated according to the following optimality criterion: whichever alignment yields the MP tree(s) with the highest consistency is considered the best alignment[ 27].
The crystal structure did not resolve the three residues closest to the N-terminus and four residues at the C-terminus, but over the remaining 448 positions, the mutual alignment yielded 95.5% identity and 98.4% similarity, which is indicative of an excellent template for comparative modeling.
The multiplicity of an alignment yields information on the repetitiveness of a genomic region.
The sequence alignment yielded a similarity of 34.3 % with almost 350 residues aligned (including gaps).
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