Align.seqs

Commands in mothur
1

Hi,

I’m encountering some problems with my alignment… Mothur gives me this with flip=F “Some of you sequences generated alignments that eliminated too many bases, a list is provided in ne.trim.unique.flip.accnos. If you set the flip parameter to true mothur will try aligning the reverse compliment as well.” And this “Some of you sequences generated alignments that eliminated too many bases, a list is provided in ne.trim.unique.flip.accnos. If the reverse compliment proved to be better it was reported.” with flip=T.

The problem is that practically all seqs are in accnos file in both cases, so they all generate weird alignment :o . What could be causing this?! I’ve tried silva and greengenes templates.

2

If you can send some of these sequences to mothur.bugs@gmail.com we can take a look. Are you certain that these are bacterial 16S rRNA sequences? Also, do the sequences include the vector?

3

Sent the seqs.

Thank you for your help :mrgreen: !

4

All your sequences are reversed. When you run align.seqs with flip=T, mothur still reports the sequences to the .accnos file, so you know which sequences were reversed. Sorry for the confusion. In version 1.13.0, releasing later this month, we added more info. to the .accnos file so it wouldn’t be as confusing.