alancleary
commented
2 years ago Done in commit 2b04b8a5dee8e9f315ef49baf52f020bd2d773bc. A side effect is that the quality of search result track alignments has improved for MSA's that had empty columns. Closing.
In the multi view, a hidden Markov model is used to multi-align the tracks before they are drawn. The final position of each glyph in a track is determined by the track's Viterbi path through the trained model. Sometimes no Viterbi paths traverse a particular match node in the model, resulting in an empty column in the micro-synteny viewer, which may lead the user to make assumptions about inter-genic distance that we don't intend. Prune these columns from the alignments.