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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

0 selected

Zach Cohen, Sandra AC3

May 29

giving up... species occurs twice in locus 1

Hello Sandy, Fantastic, replacing the ! with ? did work. The alignment was generated using macse v2,

unread,

giving up... species occurs twice in locus 1

Hello Sandy, Fantastic, replacing the ! with ? did work. The alignment was generated using macse v2,

May 29

May 28

subsitutions/site/100Mya

I have solved this problem. If anyone is ever interested feel free to contact me. Best regards, Bruce

unread,

subsitutions/site/100Mya

I have solved this problem. If anyone is ever interested feel free to contact me. Best regards, Bruce

May 28

May 28

MCMCTreeR plotting. How to plot just a few distributions?

Hi all! I am learning to use MCMCTreeR to plot results from MCMCTree. I have installed the software,

unread,

MCMCTreeR plotting. How to plot just a few distributions?

Hi all! I am learning to use MCMCTreeR to plot results from MCMCTree. I have installed the software,

May 28

张东, … Ao Qo5

May 19

Foreground species exhibit distinct amino acid residues at sites under positive selection

Hi, I've actually been encountering the same issue in my own analysis. Thanks for the

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Foreground species exhibit distinct amino acid residues at sites under positive selection

Hi, I've actually been encountering the same issue in my own analysis. Thanks for the

May 19

May 19

Help with Clade Model C in PAML: No BEB Sites Detected

Dear Professor Yang, I hope this message finds you well. I am currently using PAML (codeml) to detect

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Help with Clade Model C in PAML: No BEB Sites Detected

Dear Professor Yang, I hope this message finds you well. I am currently using PAML (codeml) to detect

May 19

Ziv Lieberman, Sishuo Wang3

May 6

Tiny question - MCMCTreeR

Sure thing! Please find attached the calibrated topology (file 'calibration_topo.trees') . I

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Tiny question - MCMCTreeR

Sure thing! Please find attached the calibrated topology (file 'calibration_topo.trees') . I

May 6

victor piñon, Sandra AC2

Apr 25

Time calibration issue

Hi Victor, Thanks for your message! I think the issue may lie in the text file you are using to

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Time calibration issue

Hi Victor, Thanks for your message! I think the issue may lie in the text file you are using to

Apr 25

Ziv Lieberman, … Sandra AC5

Apr 24

Several questions - MCMCTree/BASEML

Hi Sandy, Thank you so much for expanding on these subjects! Of course, now that you go into more

unread,

Several questions - MCMCTree/BASEML

Hi Sandy, Thank you so much for expanding on these subjects! Of course, now that you go into more

Apr 24

Saar Koene, Sishuo Wang3

Apr 1

Help with selecting alpha in codeML

Hi Sishuo, Thank you so much for your fast reply! I think I get it now. I found that the

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Help with selecting alpha in codeML

Hi Sishuo, Thank you so much for your fast reply! I think I get it now. I found that the

Apr 1

Bob Smith, Sandra AC2

Mar 20

Positive selection site detection

Hi there, Thanks for your message! You may want to look at Janet's answers and Ziheng's

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Positive selection site detection

Hi there, Thanks for your message! You may want to look at Janet's answers and Ziheng's

Mar 20

Samuel Bernardes, Sishuo Wang4

Mar 14

Help with divergence time estimation

Solved. thx for asking. further Qs, pls feel free to discuss on this forum! many people are here to

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Help with divergence time estimation

Solved. thx for asking. further Qs, pls feel free to discuss on this forum! many people are here to

Mar 14

sumei zhou, Sandra AC2

Mar 12

evolverNSbranches tree paramenter

Hi there! Thanks for your message! Please find below the answers to your question: You can use "

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evolverNSbranches tree paramenter

Hi there! Thanks for your message! Please find below the answers to your question: You can use "

Mar 12

Yihang Zhao, Sandra AC6

Feb 28

error: edid 317 / 317 site patterns

Yes, the issue is fixed! Thank you very much! Best Yihang On Friday, February 28, 2025 at 4:47:09 AM

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error: edid 317 / 317 site patterns

Yes, the issue is fixed! Thank you very much! Best Yihang On Friday, February 28, 2025 at 4:47:09 AM

Feb 28

sumei zhou, Sandra AC2

Feb 28

can evolver generate many simulations with one rootseq

Hi there, Thanks for your message. I am posting Ziheng's answer on his behalf, hope this helps! I

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can evolver generate many simulations with one rootseq

Hi there, Thanks for your message. I am posting Ziheng's answer on his behalf, hope this helps! I

Feb 28

Feb 21

Taxon sampling for PAML

Oh and one more question related to my previous question, since I plan to investigate some questions

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Taxon sampling for PAML

Oh and one more question related to my previous question, since I plan to investigate some questions

Feb 21

keigo ww, Sandra AC4

Feb 20

Issue with Divergence Time Estimation in MCMCTree: Minimum Constraint Not Respected

Hi Yiying, Yes, you must always run your analysis first without data (`usedata = 0`) to check that

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Issue with Divergence Time Estimation in MCMCTree: Minimum Constraint Not Respected

Hi Yiying, Yes, you must always run your analysis first without data (`usedata = 0`) to check that

Feb 20

Elisa Josefa González Ugalde, Sandra AC2

Feb 12

Doubts about the use of unrooted trees comparing sister species in codeML

Dear Elisa Josefa, Thanks for your message and your kind words! This is what this PAML discussion

unread,

Doubts about the use of unrooted trees comparing sister species in codeML

Dear Elisa Josefa, Thanks for your message and your kind words! This is what this PAML discussion

Feb 12

R.M.D...@salford.ac.uk, Sandra AC4

Feb 9

"Error: implement SkewN, Skewt, S2N now."

Hi Robin, I am not sure what the problem is as I do not know which binaries you are using to run

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"Error: implement SkewN, Skewt, S2N now."

Hi Robin, I am not sure what the problem is as I do not know which binaries you are using to run

Feb 9

bucek...@gmail.com, … Sandra AC7

Jan 29

mcmctree: "Error: check #seqs and tree: perhaps too many '('?"

Hi there, Thanks for your message! As the error states, you have too many parentheses in your tree,

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mcmctree: "Error: check #seqs and tree: perhaps too many '('?"

Hi there, Thanks for your message! As the error states, you have too many parentheses in your tree,

Jan 29

Maria Eduarda Lacerda, … Sandra AC6

Jan 22

Error: Seq # occurs more than once in the tree

Hi Bruce, Thanks for your message! I am not sure how your sequence alignment file was formatted, but

unread,

Error: Seq # occurs more than once in the tree

Hi Bruce, Thanks for your message! I am not sure how your sequence alignment file was formatted, but

Jan 22

Wenqiang, Sishuo Wang6

12/12/24

Detect positive selection at two branches connected to the root simultaneously?

Thanks for the reply! The initial description is misleading. The numbers of the positive selection on

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Detect positive selection at two branches connected to the root simultaneously?

Thanks for the reply! The initial description is misleading. The numbers of the positive selection on

12/12/24

Bob Smith, … Sishuo Wang3

11/28/24

ERROR: inconsistency between the following pep and nuc seqs

Hi friend, Seems that the translated seq according to your nucl seq and your input aa seq are not

unread,

ERROR: inconsistency between the following pep and nuc seqs

Hi friend, Seems that the translated seq according to your nucl seq and your input aa seq are not

11/28/24

Xuping Zhou, Sandra AC2

11/26/24

Identification of rapidly evolving genes

Hi Xuping, Thanks for your message! If the foreground branch/es are specified a priori, based on a

unread,

Identification of rapidly evolving genes

Hi Xuping, Thanks for your message! If the foreground branch/es are specified a priori, based on a

11/26/24

임원섭 / 학생 / 지구과학교육과, Sishuo Wang4

11/20/24

Some minor question regarding the output of mcmctree when using usedata = 3

Dear David, I think either out.BV or rst2 works, they should have exactly the same content. Then

unread,

Some minor question regarding the output of mcmctree when using usedata = 3

Dear David, I think either out.BV or rst2 works, they should have exactly the same content. Then

11/20/24

Louis Nastasi, Sandra AC7

11/12/24

file rst2 not found!

Hi Louis, After doing some tests, I believe that your issue may have to do with the format of your

unread,

file rst2 not found!

Hi Louis, After doing some tests, I believe that your issue may have to do with the format of your

11/12/24

keigo ww, Sandra AC2

11/1/24

mcmctree error and checkpoint

Hi Yiying, Could you please attach your input and output files, the `ckpt` file, and your control

unread,

mcmctree error and checkpoint

Hi Yiying, Could you please attach your input and output files, the `ckpt` file, and your control

11/1/24

Claire Schraidt, Sandra AC2

11/1/24

No omega in M0 model output

Hi Claire, I have just checked your attached input files and I can see that you are trying to use a

unread,

No omega in M0 model output

Hi Claire, I have just checked your attached input files and I can see that you are trying to use a

11/1/24

Tae-Kun Seo, Sandra AC2

10/31/24

What is the stopping rule for numerical optimization of PAML ?

Dear Tae-Kun, Thanks for your message! Please find below some suggestions that Ziheng has given in

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What is the stopping rule for numerical optimization of PAML ?

Dear Tae-Kun, Thanks for your message! Please find below some suggestions that Ziheng has given in

10/31/24

Carin Tarasyan, Sishuo Wang2

9/23/24

Error in paml output

Dear Karina, would you pls mind shareing the data and result files? that would help others better

unread,

Error in paml output

Dear Karina, would you pls mind shareing the data and result files? that would help others better

9/23/24

Luiz Filipe, … Sishuo Wang15

8/2/24

Use of rooted and urooted tree

Dear Luiz, Thanks much for confirming this and for initiating this interesting discussion! best,

unread,

Use of rooted and urooted tree

Dear Luiz, Thanks much for confirming this and for initiating this interesting discussion! best,

8/2/24

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