Next, we examined how the probability of error changes when conditioning on properties of interest, focusing on the case of indels that appear to be lineage-specific (LS that is, indels present in a 2× sequence but not in the other sequences according to the multiple alignments (see Materials and Methods).
CNS coordinates and sequences are provided in supplementary material files, Supplementary Material online, in FASTA format, and also multiple alignment results in supplementary material files, Supplementary Material online.
Furthermore, the reannotated trnNs of Solenopsis and L. pallens share the GTT anticodon with all of their counterparts (see the supplementary multiple alignment of trnNs, Supplementary Material online).
Multiple alignments (see Supplementary Materials Figs. S1, S2A, S2B and S3 at http://www.biology.ucsd.edu/~msaier/supmat/IntInv) and phylogenetic trees (Figs. 1A, 2 and 3) were generated for a) the full-length proteins, b) the β-barrel domains, and c) the passenger domains.
Supplementary figure S12 a, Supplementary Material online, shows an example of a multiple alignment of an identified CNS.
We also examined 5 highly curated protein families that were aligned using the Cn3D program [22] with multiple structural lines of evidence to support the inclusion of each sequence in the alignment (Materials and Methods).
We performed a multiple alignment analysis of the deduced amino acid sequences [ 29] (see Supplementary Figure S1 in Supplementary Material available online at http://dx.doi.org/10.1155/2014/424767).org/10.1155/2014/424767
We used the multiple alignment of the CYTH domain to construct phylogenetic trees using the least squares, neighbor joining and maximum likelihood methods (see Materials and Methods).
The multiple alignment of the sequence of the TM subunits used in this study was shown in supplementary figure S5, Supplementary Material online.
multiple alignment using fast Fourier transform.
