Gaps/indels, missing and/or masked characters in terminal positions
JGLAHE opened this issue · comments
How are sequence gaps/masked regions treated in Veryfasttree?
Veryfasttree threw an error that it was expecting a larger number of sequences because I had some sequences starting with gaps (coded as - characters). Recoding to ? got around this this problem, although it still gives a warning about non-nucleotide characters being present, so I'm curious about how these (and NNN/X masking) is being interpreted?
Cheers
Changing "-" to "?" should not affect anything; all non-blank unknown characters are treated as gaps. If you can provide me with an input that reproduces the error, I can check if it's a bug. Don't worry about the warnings, they should be just indicating that "?" is being treated as gaps.
Cheers
Cheers, I cannot reproduce this issue in the current release