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OSC / phylogatr-web

The web app for the Phylogatr Project - https://phylogatr.org/
https://phylogatr.org/
MIT License
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Poor quality sequences not dropped #63

Open skdecker opened 2 years ago

skdecker commented 2 years ago

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 commented 2 years ago

Here are the trimal settings being used.

https://github.com/OSC/phylogatr-web/blob/1669f21f9fb70a84e9e1466363d8ae5f1f6ec1a5/align_sequences.sh#L23

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

I'll have to look into this.