align two long sequences using Muscle but found gaps only

Question

[Pei]

Hi all:

I got two long DNA sequences (> 40k bps) from two close species, but Muscle could not produce a correct alignment of them with no error message also.

the result is an alignment made by GAPs only.

Could you please help me to find the reason ?

Thanks in advance!

[h.mon]

Basically, you are using the wrong tool for the task you want. Try Mauve, BWA (not sure if it handles 40K long sequences, though) or even Blast.

edit: also, see this thread.

[Pei]

Thanks for the reply!

[natasha.sernova]

Try to use mafft. http://mafft.cbrc.jp/alignment/software/

mafft --thread 2 --localpair --maxiterate 1000 --ep 0.123 --legacygappenalty seq4.fa > seq4.aln

version 7

Or:

mafft --genafpair --maxiterate 1000 input_file > output_file

It may help. Good luck!