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PAML discussion group

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[PLEASE READ THIS WELCOME MESSAGE UNTIL THE END BEFORE POSTING QUESTIONS AND/OR REQUESTING TO JOIN THE GROUP. REQUESTS WITHOUT ANY EXPLANATION JUSTIFYING WHY SOMEONE WANTS TO JOIN THE GROUP WILL BE REJECTED AS THEY CANNOT BE DISTINGUISHED FROM BOTS' REQUESTS]

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.

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 whether there is an issue with the format of your input files by consulting 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, please 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.; which will help us troubleshoot the issue much easier and faster.  You can find more information about how to report your warning/error messages and other issues when running software on this website.

In addition, please note that most error/warning messages discussed in this group tend to be related with input sequence and tree files and settings in the control files.  Error/warning messages do not mean that 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.).  Please consult the relevant section on the PAML Wiki so that you can check whether your input files are in the correct format based on what the error/warning messages are telling you to look for.

Lastly, as a recent security measure, please note that we are now moderating who can join the group. New users must briefly introduce themselves and explain why joining this group would help them in their research (i.e., include these details in the box where you read "reason for joining"), so that we can make sure that no bots join the group.  Please note that requests without enough information for us to verify that someone genuinely wants to join the group will be rejected.  We hope that this new restrictions can avoid future SPAM attacks and keep all subscribers safe.
  
Best wishes,
Ziheng & Sandy