Hey, good evening! I have a very large dataset of protein sequences and would like to know how I change the ClustalW source code to align a larger number of sequences? I saw that I can use the flag "--maxseqlen=n" for change the length of sequences , but I don't known how to change the number of sequences. Someone could help me? Thank you so much Mariana Rossi
I'm pretty sure you can run as much sequence data as possible through ClustalW, not that it has the memory to handle it. I do not see a flag for adjusting the memory of ClustalW. What have you tried? Have you tried to run all your data through ClustalW? You might be confined by your computer memory.
There are other aligners which are more memory efficient, such as MUSCLE, which might better suited for your large dataset of protein sequences.
It might be worth considering a different aligner if you're having problems with Clustal instead of rummaging around in its source code.
MUSCLE is pretty good at handling lots of sequences.
As others have indicated below changing programs is one option but it would only get you so far. If you truly have a gigantic dataset and need to use all of it you may need to find appropriate hardware or trim the dataset down.
Thank you so much everybody! Mariana