Hi,
I use kalign to perform MSA for DNA sequence. I used the parameter kalign -i reads.fa -f clu --tgpe 0.01 --gpo 0.2 --gpe 0.4. The input fasta file is :
Hi, I added alignment types to version 3.3.4. The dna alignment type uses standard substitution, mismatch and gap penalties and will produce a sensible alignment in the case above.
Hi, I use kalign to perform MSA for DNA sequence. I used the parameter
kalign -i reads.fa -f clu --tgpe 0.01 --gpo 0.2 --gpe 0.4
. The input fasta file is :The figure below is the alignment result of
clustalw.aln
. How can I adjust the parameter to get the similar alignment result as clustalw.Best, Neng