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!