how to adjust the penalty parameter

[huangnengCSU]

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 :

>1
GGGGGAAGGGGG
>2
GGGGAAGGGGG
>3
GGGGAAGGGGG
>4
GGGGAAGGGG
>5
GGGGGAAGGGGGG
>6
GGGGGAAGGGG
>7
GGGGGAAGGGGGA
>8
GGGGGAAGGGGGG
>9
GGGGGAAGGGGGG
>10
GGGGAAGTTG
>11
A
>12
GGGGGGAAGGGGG
>13
GGGGGAAGGGGGG
>14
GGGAGT
>15
GGGGAAGGGGG

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

[TimoLassmann]

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.