I've been wracking my brain these past few weeks to figure out why Clustal Omega gives me a segmentation fault and a core dump when I run a small number (20-30 DNA sequences) of large plasmids (>=50,000bp) through it. To my understanding, I am not going over the file size limit for Clustal to run, so it leads me to believe that this issue is due to me running very long sequences through clustal, rather than a huge number of relatively small sequences. Has anyone else tried aligning very long sequences through Clustal Omega and gotten this same error? I've been giving it plenty of memory, hundreds of Gigabytes worth, so I don't believe it is due to memory. I'm just at a loss!