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Support sequence quality annotated alignments? #8

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koadman opened this issue Oct 12, 2012 · 0 comments
Open

Support sequence quality annotated alignments? #8

koadman opened this issue Oct 12, 2012 · 0 comments
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koadman commented Oct 12, 2012

Current sequencing instruments generate a per-base quality score that are intended to estimate the probability that the nucleotide is correctly represented in the sequence. This information could be carried forward into the phylogenetic likelihood with relative ease by setting the tip partials appropriately.

Similar information could be associated with protein alignments when the sequences derive from translations of quality-annotated nucleotide reads.
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