Sentence examples for alignment we removed from inspiring English sources
After the identification of the sequences belonging to each individual and before the alignment, we removed the first five bases of every sequence corresponding to each of the barcodes.
From this final alignment, we removed the 5 sequences that showed insertions.
In the process of this manual alignment, we removed hundreds of obvious pseudogenes from outgroup sequences.
From each alignment, we removed one species at a time and used the remaining sequences to reconstruct the homolog in the removed species (target species) with the maxAlike algorithm using the phylogenetic tree from the multiz phastCons model (see Supplementary Fig. S13).
To enlarge the alignment, we remove all mapped nodes from after the execution of Step1 and Step2, restore all the homological similarity edges and repeat both steps.
From these alignments we removed all codons from poorly aligned regions or those with insertion/deletions.
We used the ClustalX option "Iterate each alignment step," which significantly improved the alignment, and we removed all gaps before each realignment.
We suspect that repeats make these intervals difficult for read alignment, so we removed any SVs from these regions.
After multiple sequence alignment (MSA) using MUSCLE, we removed partial, duplicated or highly divergent (likely to be sequencing errors or incorrect spliced products) peptide sequences, after which 148 peptide sequences remained in the final multiple sequence alignment (Additional file 6: Figure S4).
We removed alignments with frame shifts and the remaining alignments were confirmed visually.
Sometimes no conserved regions were found within our search limits, in which case we removed alignments with the lower vertebrates (F. rubripes and D. rerio) and only analyzed alignments to G. gallus and/or X. tropicalis to find conserved non-coding regions.
