Aligning sequences of different lengths with MEGAX CLUSTALW

Question

[itsmarina.n]

I have tried to align sequences from the FASTA file in MEGAX software. I left the software to run for 7 hours and it did not end it, it stopped at site conservation 100 and it was still running. I found out that the problem is that sequences are not the same length and that CLUSTALW could be a solution. But, I cannot start CLUSTALW. When I go to Align -> Edit/Build Alignment -> Retrieve data it just starts immediately to do aligning, I guess in the same way as before. Then, I clicked on Alignment -> Align with CLUSTALW, but nothing changes. It seems like it is doing just the ''regular'' alignment again. I do not understand what is going on, I have looked at the MEGAX help page, but it does not help me understand the issue.

Did the type of alignment change, but it just looks the same as when I did not start CLUSTALW? I am a beginner so I do not know how long these alignments should take (I have around 10 000 sequences with really varying lengths - from one million to 500 base pairs)

Thanks in advance!

Answer 1

[Mensur Dlakic]

Very few programs are meant to align 10 thousand sequences, and even fewer are meant for aligning sequences that have on the order of millions of bases. Don't know exactly what you are trying to do, but it is almost a guarantee that aligning sequences in that size and length range will take a very long time. It is also a near-guarantee that such an alignment will not be meaningful. I think you might want to define your problem better by narrowing the number of sequences to something more manageable and in a more uniform range of sizes.