This alignment comprises seven nuclear housekeeping genes (aldolase, methionine adenosyltransferase, ATP synthase beta chain, catalase, elongation factor 1 alpha, triosephosphate isomerase and phosphofructokinase; [ 37]) and three ribosomal DNAs (5.5S, 18S, and 28S rDNA) from 119 taxa.
This alignment comprised three contiguous hits covering the top 14% of Mt-6 then a separate set of three contiguous hits that aligned with the bottom segment of Mt-6.
After indels and poorly aligned positions were removed the alignment comprised 15,685 bp including 6,986 informative sites.
Among the 3,562 bp, the alignment comprised 1,627 45.688%) variable sites, of which 1,392 39.088%) were parsimony informative.
For example, the test for an artificial attraction of Ectoprocta and Phoronida due to a deviating amino acid composition is based on a subset of the alignment comprising the character states at all positions where the ancestor of the Ectoprocta + Phoronida clade is characterized by apomorphies.
The resulting 123 taxa prank alignment comprises 9,027 aligned positions and 2,051 positions past trimming.
Nevertheless, although the assembled sequence presents the conserved regions characteristic of the protein family of both animals and fungi, the region of alignment comprises less than 60% of the total length of the best matching sequence.
This concatenated alignment comprised 6,436 amino acids (data set c24p, 24 CDS; gene no. 1 24 in supplementary table S3, Supplementary Material online).
The RPE alignment consisted of 183 alignable characters and the GAPDH alignment comprised 278 alignable characters.
In the original NAST implementation, each user-submitted candidate sequence is aligned to the Greengenes 'Core Set' (a template alignment), comprising approximately 5000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea.
After removing unreliably aligned regions, the final alignment comprised 150 taxa and 1,647 positions (the alignment is available upon request).
