All alignment columns containing ambiguities and gaps were excluded during the PAML analysis.
Non-contiguous sequences (those annotated as "fragments"), sequences containing ambiguities and exact duplicates were removed using a Perl script.
In some (e.g. inbred) species where homozygous individuals are common, direct sequencing is very useful, and eventually, "heterozygous sequences" may be deduced automatically from sequence files containing ambiguities, using dedicated software [ 23, 24].
Defining user expectation and meeting them is important to solve this problem, which naturally contains ambiguity and vagueness.
Sequence portions that were not represented among all samples, contained gaps, and/or contained ambiguity codes were removed using the "strip alignments" feature in Geneious (Fig. 1).
Both of these details contain ambiguity that potentially undermines the practical application of the Act: what constitutes clearly distinguishable or special characteristics and how to ensure that the special characteristics are not altered.
We avoided simply aligning the sequencing reads to the consensus sequences for the repeat classes since transcripts originating from older or slightly divergent members of a class of repetitive elements may be missed using this approach, and many of the consensus sequences contain ambiguity characters.
Phylogenetic and taxonomic studies of viruses based on complete genome data have become increasingly important as more and more whole viral genomes are sequenced [ 2- 6] The phylogeny based on single genes or gene families contains ambiguity because horizontal gene transfer (HGT), along with gene duplication and gene capture from hosts, appear to be frequent in large DNA viruses [ 7- 10].
Barcelona's alignment with Catalanism is less ambiguous (but still contains ambiguities) and the club boasts a social and political power that is gigantic.
"The notification was not very pleasant," Father Dupuis, 77, said of a Vatican document published on Monday that concluded that his writings on religious pluralism "contained ambiguities" about doctrine that could lead readers to "erroneous or harmful positions".
