Poor quality sequences not dropped

[skdecker]

I have noticed in some recent downloads that there are sequences included in the alignment that likely should have been dropped during the filtering process. In the two attached plots of alignments the first sequence(s) is nearly all missing data and the small number of base pairs that are in the sequence don't seem to align particularly well. Could this be an error with the TrimAl portion of processing?
Batrachuperus-pinchonii-COI.pdf
Hynobius-amjiensis-COI.pdf

[johrstrom]

Here are the trimal settings being used.

phylogatr-web/align_sequences.sh

Line 23 in 1669f21

bin/trimal -in $1 -resoverlap 0.85 -seqoverlap 50 -gt 0.15

sequences included in the alignment that likely should have been dropped during the filtering process.

I'll have to look into this.