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We note that in the HIV data set alignment uncertainty does not significantly effect the topology posterior.
Due to the low variability and non-overlapping occurrence of gaps in the data set, alignment, assessment of homology and subsequent coding of gaps was straightforward.
defer.add img); Set Alignment.
The other input set is scanned against this indexed set, alignment seeds are generated, some aligners extend these seeds, and finally a dynamic programming function is used to join seeds that are adjacent and to generate an alignment score taking in consideration read errors, SNPs and/or small insertion or deletions (micro indels).
For C5, besides diversity in the feature set, alignment scores of conserved regions turned out to be very useful.
The anchored alignment had 1,094 positions for 296 taxa, with four taxa without ITS1 regions excluded from the whole ITS data set (Alignment S4).
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After the first training pass through the full 110-h data set, alignments and lattices are regenerated and two more epochs are performed at a constant learning rate.
These promoters were processed to obtain a background MCR set, alignment-free regions, and combined conservation sequences.
For the second (Type2.2) and third (Type2.3) sets alignment identity criteria was relaxed to 50 and 35%% respectively [ 41].
Although the Hidden Markov Model used for the alignment is based on an extensive training set, the alignment did require some manual optimisation.
When the alignment candidate threshold is set, only alignments reaching at least the set length are considered.
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