Natural scienceBioinformaticsBioinformatics algorithmsPhylogenetics

Phylogenetic tree construction

Theory

What to do with gaps?

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Match best decisions on "what to do with gap regions".

Match the items from left and right columns
Gaps are in the middle of alignment. In the portion of sequences there are continuous bands of characters in these gap columns that look like insertions.
Gaps are in the end of alignment and there are definitely no insertions.
Gaps are in the middle of alignment. There are no obvious insertions, but some sequences have short continuous bands of characters.
Most certainly remove.
Construct two trees with and without gap columns. Try to analyze more closely gap columns region in the middle.
Most certainly retain.
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