Orthologous non-coding sequences were aligned using Owen [ 53], to generate global alignments consisting of segments with significant sequence similarity (p < 0.001), also called hits, interspersed with segments for which sequence similarity was below that significance threshold.
The main alignments consist of more than 3,000 granite menhirs, arranged in rows between 3300 BC and 1500 BC.
For alignments consisting of n truly i.i.d.i.d
The alignments consist of homologs from the annotated Dscam genes and the new homologs we found.
The alignments consisted of single gene data, concatenated SSU + LSU and concatenated SSU + LSU + EF2 data.
From the initial alignments, the 6,661 sequence alignments consisting of fewer than 15 taxa were discarded; leaving 75,368 alignments.
Only 67 false positives were expected in the human-chimpanzee alignments consisting of 2.4 Gb of alignment sites.
Final truncated alignments consisted of 268 and 208 sequences of 614 and 319 nucleotides in length, for COI and EF1a, respectively.
We also executed several additional alignments consisting of only those bHLH sequences that belong to a particular family from 6 insect species above mentioned (Additional file 4).
We used COMPASS and PHOG-BLAST to find BBHs between these two databases each having 500 alignments consisting of 3 sequences.
