Sep 11, 2020, 8:39:37 AM9/11/20
I'm trying to align two sequences, where the first aligns perfectly to
the end of the second. T-Coffee, however, insists in aligning the first
two nucleotides (CC) of seq 1 to the beginning of the seq2 (AA). I
checked this both in the online version and the installed linux version,
t_coffee test.fa -type rna -output fasta
I'm playing around with the gapopen and gapext but this doesn't fix the
problem and I feel like I should not need to do that at all - the
correct alignment should be absolutely clear.
Am I missing something?
It would be great if someone could help.