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Hi PAML Users,
 
Welcome to the PAML discussion group!  This site is for posting questions and discussions of the PAML software package.  PAML stands for Phylogenetic Analysis by Maximum Likelihood.

Most error/warning messages discussed in this group tend to be related with input sequence and tree files and settings in the control files.  Please note that error/warning messages do not mean that the PAML programs are not working; they tend to inform users about possible issues with their input files (e.g., mismatched sequence names in input sequence file and input tree file, wrong format for the sequence names, etc.).  To help you navigate the PAML documentation, we have created a PAML Wiki on the PAML GitHub repository so that you can verify whether your input files are in the correct format based on what the error/warning messages are telling you to look for.

Before posting a message, please use the search tool in this PAML discussion group and type keywords related to your issue to check whether your question/s have already been asked by other PAML users.  You should also refer to the FAQs document and check the format of your input files in the PAML Wiki.  If you still cannot find an answer to your question/s, please post them in the PAML discussion group.  When doing so, please do not just paste the screen output and the error/warning messages that you get without any more details.  Instead, make sure that you attach the input files and the control files you are using, explain how you ran PAML, which PAML version you are using, etc. In that way, your issue will be much easier and faster to troubleshoot.  You can find more information about how to report your warning/error messages and other issues when running software on this website.
  
Best wishes,
Ziheng