gravatar for Mensur Dlakic

1 hour ago by

USA

I don't think you will fix this by changing environmental variables like you attempted. I think you need to recompile the whole program to allow for larger number of sequences. You get the package from here and inside the file coffee_defines.h change the 260000 to something larger, say 500000. Run the ./install script after that and it should create a new t_coffee that will be able to work with larger number of sequences. There is a more detailed description on how to do all of this on their website.

I will mention that aligning >400000 sequences in any program will take a very long time, and it may not be practical to wait for it. You may need to consider using fewer sequences.



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