We inspected the taxonomic assignments of all ORFs that resided on the same scaffolds as the viral sequences in question and the occurrence of each viral, bacterial, eukaryotic, and archaeal sequence was documented.
Even though it is known that porosporids use bivalve species as intermediate hosts, their developmental stages in the bivalves are found in the blood not in the intestine [64] [65]; moreover, the sequences in question are associated with the subclade containing the Cephaloidophoridae not with the subclade of putative porosporids.
The sequences in question have lengths ranging from 0.6 Mbp to 8 Mbp, accounting for a total 48 Mbp.
To verify the linkage mapping the SNP-containing sequences in question were mapped onto the IMpRH7000 panel (Additional file 1).
We have removed 113 sequences in question from the databases and apologize for any inconvenience this might have caused.
To use this program, a multiple sequence alignment was first constructed of the sequences in question using the MUSCLE server [ 42].
For instance, a common and powerful method of determining genetic relationships is to utilize a global alignment of sequences in question and perform a maximum likelihood comparison.
This is problematic because the probabilities of each misclassification will rarely equal each other and are conditional on the level of divergence of the two sequences in question.
It is not surprising that the two sequences in question have individually diverged a significant amount from the original sequence of the common ancestor at that locus.
This is for good reason; such covariation can be difficult to identify, even when the sequences in question (as in the case for RPB1) have relatively well-characterized functions and biochemical interactions [ 37].
The most obvious, is that the sequences in question are related to known Apis proteins, but they mainly contain untranslated regions (UTRs) and therefore do not produce significant "hits" in BLASTX alignments.
