Running Paml (CODEML) on batch mode ?
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6 weeks ago
sunnykevin97 ▴ 970

HI,

I had 5000 ortholog sequences to be tested using codeml.

Using the ndata option in codeml, I'm only able to run upto 10 sequences at a time in one go. More than 10, the codeml crashes and ends up in segmentation fault error.

Segmentation fault error is not because of memory issues, codeml can handle up to 10 sequences at a time. Another option is to use a bash or python script.

Does any have an easy understandable code for automating the codeml analysis ?

Suggestions appreciated.

Thanks

gene genome protein • 175 views
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