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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

0 selected

Dilrini Vanrooyen, Sandra AC2

Apr 17

MCMCTree error: Only bounds for the root age are implemented..

Hi there, Thanks for your message! It seems that there may be various problems regarding the format

unread,

MCMCTree error: Only bounds for the root age are implemented..

Hi there, Thanks for your message! It seems that there may be various problems regarding the format

Apr 17

Li Edwin, Sandra AC3

Apr 11

How to determine the positive selection and purifying selection based on codeml output

Hi Sandra, I appreciate your useful explanation! Your assumption is right. I'm testing for

unread,

How to determine the positive selection and purifying selection based on codeml output

Hi Sandra, I appreciate your useful explanation! Your assumption is right. I'm testing for

Apr 11

Jules, … BMG5

Apr 11

nan error in rst file

Dear Ziheng, I hope this message finds you well. I am revisiting results from an older codeml run (v4

unread,

nan error in rst file

Dear Ziheng, I hope this message finds you well. I am revisiting results from an older codeml run (v4

Apr 11

Jingliang Kang, Sishuo Wang3

Apr 5

How to estimate branch lengths, amino acid frequencies and the best shape parameter for variable rates among sites (alpha)

Dear jingliang, I think the above was partly wrong by saying "i am unsure if codeml allows

unread,

How to estimate branch lengths, amino acid frequencies and the best shape parameter for variable rates among sites (alpha)

Dear jingliang, I think the above was partly wrong by saying "i am unsure if codeml allows

Apr 5

BMO, Janet Young2

Apr 4

How to run PAML command line in the background in Linux system

not sure if this will work, but try it and let us know: "nohup /home/software/paml-master/src/

unread,

How to run PAML command line in the background in Linux system

not sure if this will work, but try it and let us know: "nohup /home/software/paml-master/src/

Apr 4

박현선, Sandra AC2

Apr 3

Resolving codeml Analysis Issues with Non-Multiples of Three in Sequence Length

Hi there, Thanks for your message! I am not sure what could have gone wrong during the filtering

unread,

Resolving codeml Analysis Issues with Non-Multiples of Three in Sequence Length

Hi there, Thanks for your message! I am not sure what could have gone wrong during the filtering

Apr 3

pasca...@gmail.com, Sandra AC5

Apr 3

strange calibration

Yes, understood - thank you! I was just briefly reporting back here, in case others found themselves

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strange calibration

Yes, understood - thank you! I was just briefly reporting back here, in case others found themselves

Apr 3

Maya G, Sandra AC6

Mar 28

check #seqs and tree: maybe too many '('

Hi there, It seems that you had double brackets to specify a clade (ie, same clade was repeated twice

unread,

check #seqs and tree: maybe too many '('

Hi there, It seems that you had double brackets to specify a clade (ie, same clade was repeated twice

Mar 28

guo, Sandra AC6

Mar 19

MCMCTree error: raise NS?

Glad that it worked in the end! All the best, S. On Tuesday 19 March 2024 at 05:52:01 UTC guo wrote:

unread,

MCMCTree error: raise NS?

Glad that it worked in the end! All the best, S. On Tuesday 19 March 2024 at 05:52:01 UTC guo wrote:

Mar 19

Lulu, Sandra AC2

Mar 19

Interpret omega values for significant log likelihood test?

Hi there, If the result of the LRT led to your null hypothesis being rejected (eg, "ω does not

unread,

Interpret omega values for significant log likelihood test?

Hi there, If the result of the LRT led to your null hypothesis being rejected (eg, "ω does not

Mar 19

冉冉, Sandra AC2

Mar 18

Codeml has been killed when running the software.

Hi there, It looks like there are various formatting issues in your input files: 1) The format of

unread,

Codeml has been killed when running the software.

Hi there, It looks like there are various formatting issues in your input files: 1) The format of

Mar 18

Lulu, Sandra AC5

Mar 18

branch and branch-sites tests yield different results

Hi Lulu, There is not a unique answer to your questions, hence why this is part of the biological

unread,

branch and branch-sites tests yield different results

Hi Lulu, There is not a unique answer to your questions, hence why this is part of the biological

Mar 18

Amber Nashoba, Sandra AC4

Mar 11

Hi Amber, I have just had time to check your input files now, apologies for the delay. It seems that

unread,

Hi Amber, I have just had time to check your input files now, apologies for the delay. It seems that

Mar 11

Mar 6

Estimated parameters for Mutation-Selection model

Dear Ziheng, I'm trying to look at estimated parameters with Mutation-selection model of Yang and

unread,

Estimated parameters for Mutation-Selection model

Dear Ziheng, I'm trying to look at estimated parameters with Mutation-selection model of Yang and

Mar 6

Janani Hariharan, … nathanael....@gmail.com6

Feb 27

error: end of tree file

This does solve my issue, thanks for the help and the handy documentation link! On Monday 26 February

unread,

error: end of tree file

This does solve my issue, thanks for the help and the handy documentation link! On Monday 26 February

Feb 27

Miles Zhang, Sishuo Wang6

Feb 26

MCMCTree analysis not starting

Dear Miles, Could that be bc on hpc the output may be stored before being presented to the user? I am

unread,

MCMCTree analysis not starting

Dear Miles, Could that be bc on hpc the output may be stored before being presented to the user? I am

Feb 26

ke yang, … Ziheng4

Feb 22

MCMCTree Error: oom p2s or zt.

i took a look at the code that generated the error message. "oom" is my short form for

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MCMCTree Error: oom p2s or zt.

i took a look at the code that generated the error message. "oom" is my short form for

Feb 22

Saam Hasan, Sandra AC2

Feb 22

Hi there, The idea is that large values for dS may mean saturation so that the precise value is not

unread,

Hi there, The idea is that large values for dS may mean saturation so that the precise value is not

Feb 22

Szabi Kormány, Sandra AC2

Feb 22

Codeml parameter set-up.

Hi there, As far as I am concerned, pamlX is not maintained anymore, and this issue might be related

unread,

Codeml parameter set-up.

Hi there, As far as I am concerned, pamlX is not maintained anymore, and this issue might be related

Feb 22

bilge, Sandra AC3

Feb 22

fix omega during the batch run

Hi there, I believe there may be a problem with your control file (and, possibly, with your input

unread,

fix omega during the batch run

Hi there, I believe there may be a problem with your control file (and, possibly, with your input

Feb 22

bilge, … Ziheng4

Feb 9

codeml memory problem

this did not work, but i tried the upper answer and it worked, thank you both so much 9 Şubat 2024

unread,

codeml memory problem

this did not work, but i tried the upper answer and it worked, thank you both so much 9 Şubat 2024

Feb 9

Bruno Gomes, Sandra AC2

Feb 7

How should I interpret this?

Hi Bruno, You may want to look at Janet's answers and Ziheng's answers to two similar

unread,

How should I interpret this?

Hi Bruno, You may want to look at Janet's answers and Ziheng's answers to two similar

Feb 7

Skip, Sandra AC2

Feb 5

error: maintree file can have only one tree

I believe this is a duplicate, I gave an answer to this question here: https://groups.google.com/g/

unread,

error: maintree file can have only one tree

I believe this is a duplicate, I gave an answer to this question here: https://groups.google.com/g/

Feb 5

Kelly, … Skip6

Feb 5

Error: maintree file can have only one tree.

Thank you. I've been using the R package MCMCtreeR since this is such large and unwieldy tree. I

unread,

Error: maintree file can have only one tree.

Thank you. I've been using the R package MCMCtreeR since this is such large and unwieldy tree. I

Feb 5

Y DD, Sishuo Wang6

Feb 5

MCMCTREE problem: Error in sequence data file: E at 61 seq 1.

No problem now, I found that there were no errors when 'ndata = 1' was set in the '

unread,

MCMCTREE problem: Error in sequence data file: E at 61 seq 1.

No problem now, I found that there were no errors when 'ndata = 1' was set in the '

Feb 5

Yihang Zhao, Sandra AC2

Feb 4

Which result should I trust, NEB or BEB, and why?

Hi there! As it has been explained in various articles (eg, Yang et al. 2005, Álvarez-Carretero et al

unread,

Which result should I trust, NEB or BEB, and why?

Hi there! As it has been explained in various articles (eg, Yang et al. 2005, Álvarez-Carretero et al

Feb 4

david....@gmail.com, … Ziheng4

Jan 26

Time unit sensitivity of the birth-death model?

Hi Sandra, Ziheng, Many thanks for your detailed and informative replies! I guess what confused me

unread,

Time unit sensitivity of the birth-death model?

Hi Sandra, Ziheng, Many thanks for your detailed and informative replies! I guess what confused me

Jan 26

dvd, Sandra AC2

Jan 23

failure in reconstructing ancestor sequences

Hi there, It seems that you are not specifying the location of the `jones.dat` file. Note that you

unread,

failure in reconstructing ancestor sequences

Hi there, It seems that you are not specifying the location of the `jones.dat` file. Note that you

Jan 23

Janani Hariharan, Sishuo Wang2

Jan 11

pal2nal produces blank output with nogap

Dear Janani, thx for the question! I don't think your AA seq is aligned but you're that even

unread,

pal2nal produces blank output with nogap

Dear Janani, thx for the question! I don't think your AA seq is aligned but you're that even

Jan 11

Banisha Phukela, Janet Young8

Jan 3

error in codeml data analysis

It's a bit unclear what it is you really want to learn from your sequences. You used model=2,

unread,

error in codeml data analysis

It's a bit unclear what it is you really want to learn from your sequences. You used model=2,

Jan 3

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