I didn't use the align_seqs since I aligned with MAFFT. Muscle would not work on a denovo alignment of ~17,000.
Referring to this post
, I just have a question regarding the use of the filter_alignment script (I am using QIIME 1.8). There appears to be a bug in the script when I use the -r option. So I am just using -g and -e to filter gaps and highly entropic bases at 5%. Do I have to put the arguments in a certain order or use the entropy threshold of 0.0005 as it is mentioned int the post? My alignment lengths were almost 800bp, and they got filteredis filtered down to 300bp, which is close to the amplified gene length. I just put -g 0.9 -e 0.05 as gaps are removed first. I chose the entropy of 0.05 based on the sequence length.