Sentence examples for gaps were coded from inspiring English sources

Gaps were coded as separate characters.

For all ITS and CR alignments, gaps were coded as present or absent using the "simple" gap coding method employed in GapCoder v1.0 [35].

Gaps were coded as missing characters in the initial analyses, but were also coded with the program SeqState [113], using the simple coding (SIC) of Simmons and Ochoterena [114].

Terminal gaps were coded as missing data.

Gaps were coded as missing data.

All gaps were coded as missing data.

Moreover, under parsimony criteria the position of myxozoans is dependent upon how gaps are coded: if gaps are coded as a fifth character state, myxozoans are placed as a highly derived clade of bilaterians (Additional file 4); if gaps are coded as missing, myxozoans are placed as sister to all metazoans (Additional file 5).

For example, it is easy to define a format for nucleotide data where gaps are coded as a fifth state or for binary data.

The best alignments, in which there are no gaps in the query or subject alignments are color coded in red; the next best alignments, that have subject gaps but no query gaps are coded in green; the third category, in which there are both query gaps and subject gaps are coded in blue and the poorest category, that contains query gaps as well as mismatches, is coded in black.

On the other hand, if the gaps are coded separately (e.g., as BC), then the phylogenetic signal present in the gaps (if the alignment is accurate) increasingly becomes the only information for the inference method to rely on, as G/S increases.

Sequences with gaps that extend beyond both the 5'- and 3'-termini of the gap being coded, as well as sequences with gaps that extend beyond one terminus and to the other terminus, are scored as missing data for that character.