I am trying to do evolutionary analysis of around 125 CDS alignments using PAML software; it kills the analysis just after few seconds of running. I have used different software to make".phy" format file. The problem has not been solved yet.

Also using Data monkey was not helpful at all; seems I need to remove all stop codons in my sequences regardless of their positions and then run data monkey! any idea how?

Thanks in Advance for your suggestions.

Mah

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