Unreliable sequence alignment loci were removed using Gblock version 0.91 bb).
Because the interval between seeds is longer, less seeds are used to identify candidate mapping locations, and with the default of no mismatches allowed within a seed some correct alignment loci would not be considered.
Moreover, multiple alignments between the rag locus and Sus showed that the RagA and SusC were both constituted of three domains (TonB I, II, and III); and RagB and SusD were constituted of two domains: Lipoprotein and RagB/SusD, respectively.
The 3s program currently uses just one sequence per species at each locus, and it removes alignment gaps and ambiguous nucleotides from the alignment.
Based on the generated alignments, locus-specific primers were constructed, with the forward primer occupying a region 5'-end upstream of the insertion site, which is conserved among the colobine and human or chimp sequences.
First, using a subset of terms from the Gene Ontology (GO Slim) [ 48] we grouped 2,158 alignments (loci) containing GO annotation into 27 broad classes as defined by their parent GO terms from the Molecular Function ontology.
After manual inspection of alignments containing nonsense SNPs, to filter out cases that could be explained by genome assembly problems, we ended up with 113 alignments (loci) with clear nonsense polymorphisms, many of which correspond to hypothetical proteins (80%, see Additional file 3: Table S3).
Full nexus alignment of 13 loci and 250 taxa, and relevant data partitions.
Two loci in different replicons are considered homologous if, for both loci, the region of overlap between the BLAST alignment and the locus is i) more than 50% of the entire length of the locus, ii) more than 80% of the entire length of the BLAST alignment, or iii) longer than 75 bp.
We ran separate analyses on each locus and on the concatenated alignment.
