ChromA provides a number of visualizations for alignments, variable data and chromatograms, which are generated using the open source library JFreeChart (Gilbert and Morgner, 2009).
The data set contains 10 variable sites and 6 informative sites under the Clustal W alignment, 12 variable and 7 informative sites under the Muscle alignment, and 11 variable and 6 informative sites under the MAP estimate from the joint model (Table 1, – Indel contribution).
In the protein alignment, 11 variable residues are VirB4a-specific, whereas 43 variable residues are unique to VirB4b, illustrating more conservation of VirB4a with non-Rickettsia proteins.
We observed 78 variable sites within the concatenated 1112-bp cyt b and D-loop sequence alignment (41 variable sites from cyt b and 37 from D-loop), which resulted in 94 unique haplotypes among the 234 Dunlin specimens examined (Appendix B; GenBank accessions for D-loop: KP205084– KP205177; GenBank accessions for cyt b: KP205178– KP205178).
Although the characteristic TIRs and TSDs of the five β-amylase elements are easy to align, the regions between the TIRs (excluded from Fig. 1 alignment) are variable in both length and sequence (Fig. 2).
The primers were designed, by multiple sequence alignment of variable regions, specific for cold-adapted donor virus HTCA-A101, as compared to other influenza A viruses.
Additional file 5: Alignment of variable domains from SCAmpPs-3 and -4 promoters 130 bp 5′ to the transcription start.
CDD [ 46] provides a collection of PSSM profiles for Pfam families and MulPSSM [ 47] is another related resource that use multiple PSSMs corresponding to a given alignment and variable reference sequences.
The program snp-sites was then used to code missing data and SNP sites from ambiguous sites within the consensus sequences and create an alignment containing variable sites (https://github.com/andrewjpage/snp_sites).
Strong between- and/or within-population differentiation of haplotypes indicative of local or partial selective sweeps are observed in the alignment of variable sites in candidate genes harboring the strongest signals (e.g. Additional file 8: Figure S8).
