RepeatScout was used to construct consensus sequences representing fragments of ancestral elements from all shotgun reads masked by each family; multiple divergent consensus sequences mapping to the same TE region represent different subfamilies (Macas et al. 2007).
Phylogenies of the remaining 32 proteins represented by 49 K. brevis EST contigs could not be clarified due to the presence of multiple, highly divergent sequences in different protist lineages that might have resulted either from independent gene transfers or from ancient gene duplications.
Plant species and hybrid and polyploid ones in particular, often contain several rDNA loci with multiple divergent ITS sequence types.
We have used ClustalW (www.ebi.ac.uk/clustalw), a general purpose multiple sequence alignment computer software for proteins, which produces biologically meaningful multiple sequence alignments of divergent sequences.
In order to investigate the evolutionary relationship of the CID sequences from different lineages of life, the ClustalW2 program (http://www.ebi.ac.uk/Tools/clustalw2/index.html) was performed with the sixty CID sequences, because the program can produce a multiple sequence alignment of divergent sequences and Cladogram or Phylogram to visualize the evolutionary relationships [75].
The inclusion of sequences from multiple, divergent species sharing a commonly derived phenotype improves the resolution of comparative sequence analysis.
Divergent sequences between multiple overlapping contigs in these 6 regions indicated at least 2 different strains.
This "simple" model is potentially useful for large data sets with short (in this case, highly divergent) sequences when multiple parameter estimates are expected to have high associated variances [e.g., [ 57, 58]].
Strikingly, the monoallelic or biallelic variants carried in multiple human TNF promoter SNPs match divergent sequences in the primate lineage.
The two synthetic H1N1 hemagglutinin (HA) plasmids, tested in the current phase 1 study, incorporate sequence information from multiple divergent strains.
