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The pair wise-deletion option was used to treat gaps in the alignment of GPAT, LPAT or DGAT sequences.
In addition, it is important to treat gaps by pairwise-deletion rather than complete-deletion, i.e. ignoring only those gaps that are involved in the comparison of a pair of sequences because random insertions or deletions were frequent in the evolution of the two viral genes especially among different subtypes.
The MONKEY (Moses et al., 2004) and rMonkey (Moses et al., 2006) algorithms treat gaps as mistakes in the multiple alignment.
Similar(57)
Prior work demonstrated the improvement of peripheral nerve regeneration in gaps implanted with collagen scaffold-filled collagen tubes, compared with nerve autografts, and the promise of such implants for treating gaps in spinal cord injury (SCI) in rats.
ML analyses treated gaps as missing data.
MP analyses were performed treating gaps as missing data and as a 5th state.
The maximum number of differences resulting from single substitutions among haplotypes was calculated with 95% confidence limits, treating gaps as missing data.
Treating gaps as missing data, the phylogenetic trees of 14 taxa in Zea based on ITS sequence variation were constructed, and rooted by Tripsacum species (Trip).
The maximum number of differences among haplotypes, as a result of single substitutions, was calculated with 95% confidence limits and treating gaps as missing data.
ML and BA treated gaps as missing data.
RaxML treats gaps as missing data, so that might also account for the differences.
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