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  • Guide Trees for 100K sequences and Custom PSSMs

    Hi,

    I have a group of antibody sequences that I know should not produce insertions or deletions as I know they come from the same ancestor. Using MSA software like clustalw this is easy by just setting the gap scores to something extremely high. However, I'm getting segmentation faults for large amounts of sequences (>100K). Does anyone have any idea how to mitigate this or have a suggestion for another MSA program to use?

    My second question is entering custom PSSMs. It seems that you can enter your own PSSM using clustalw as well but I can't find any documentation on how I would do that.

    My end goal is to show two phylogenetic tree's. One from a guide tree produced using just a standard PSSM like PAM30, and the other using my custom PSSM that I produced with some structural information.

    Can anyone begin to tell me where to look for this information?

    J

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