I am doing multiple sequence alignment using ClustalOmega for 600 dna covid-sequences with input characters around 30574 characters for each sequence. I am running it on windows cmd. I defined parameters in input of maxseqle = 37000, however, the output each time gives duplicated length around 75000 charcters per each sequence.
clustalo.exe -i Allseq.fasta --is-profile --use-kimura --seqtype DNA --maxseqlen 37000 --threads 8 -o myclustalv3.fasta
How can I solve this problem, what will I define in input parameters. This problem occurs with large no of sequences 600 sequences. In test of 40 seq, it gave me normal output length around 32000 characters but when align all 600 sequences together, it gave this duplicated length results.
If you don't know how to use the parameters, just don't use them. In this particular case, dont use any parameter for sequence length. And thats is not error, it appears error to you because of your interpretation.
Abhijeet Singh I did before the analysis without any parameter and gave me the same duplicated length
You are the first ever to get concern about the resulting length of an alignment. It is also strange to me because what ever you are trying to do and whatever you mean with the duplicated length, does not make any sense.
Abhijeet Singh I concern the length because I am doing comparative analysis betweem Muscle,Mafft and ClustalOmega and the length of clustal is totally different than the others which made the analysis of alignment is totally different
Artur Burzynski
Sure, my question is after our discussion. Anyway, the author of clustal-Omega replied me to modify the input parameters and check the identifiers. Thanks a lot.- Badges
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