PAML discussion group

1–30 of 922

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.

I am sorry that the previous site at UCL was down for quite a while and is now taken out of service forever. As a result we have lost all the past posts. Unfortunately this is the second time I had to move the PAML discussion site.

Anyway, please post your questions about PAML programs here.

Best wishes,

Ziheng

0 selected

Tiago Simoes, Sishuo Wang3

5:23 AM

GTR model in mcmctree

Hi Tiago, forgot one thing. you might also want to set getSE = 2 in baseml.ctl so that the gradient

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GTR model in mcmctree

Hi Tiago, forgot one thing. you might also want to set getSE = 2 in baseml.ctl so that the gradient

5:23 AM

May 30

codeml: error in tree file

Hi all, I am trying to run different models on three different genes using codeML. I used MUSCLE to

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codeml: error in tree file

Hi all, I am trying to run different models on three different genes using codeML. I used MUSCLE to

May 30

kim.ve...@gmail.com, … Sandra AC5

May 12

Correct way to do LRT statistics?

Hi Denis, I just saw the other message that was addressed to Kim, but just realised it might have

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Correct way to do LRT statistics?

Hi Denis, I just saw the other message that was addressed to Kim, but just realised it might have

May 12

sima rout, … Carin Tarasyan4

May 10

PROBLEM IN RUNNING PAMLX

ohk. got it. Thank you so much for your kind response. On Wednesday, May 10, 2023 at 3:15:46 PM UTC+5

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PROBLEM IN RUNNING PAMLX

ohk. got it. Thank you so much for your kind response. On Wednesday, May 10, 2023 at 3:15:46 PM UTC+5

May 10

Alexis Gagnier-Michel, Sandra AC2

May 10

PamlX: failed to launch process

Hi there! Check that you have given executable permissions to the PAML programs inside the `bin`

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PamlX: failed to launch process

Hi there! Check that you have given executable permissions to the PAML programs inside the `bin`

May 10

Scott Brainard, Sandra AC2

May 10

Using data from many single copy orthologs to build single tree

Hi Scott, I believe you are using the wrong format for the input files. Not sure which PAML program

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Using data from many single copy orthologs to build single tree

Hi Scott, I believe you are using the wrong format for the input files. Not sure which PAML program

May 10

May 9

How to filter dn/ds of free-ratio model

Dear, All I am currently conducting a free-ratio model analysis using NCBI's primate ortholog

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How to filter dn/ds of free-ratio model

Dear, All I am currently conducting a free-ratio model analysis using NCBI's primate ortholog

May 9

金森駿介, … Yangkang Chen5

May 3

Detecting the convergent adaptative evolution by using branch-site model.

Hi Kanamori, I'm facing the same problem. How did you finally solved that? On Tuesday, October 24

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Detecting the convergent adaptative evolution by using branch-site model.

Hi Kanamori, I'm facing the same problem. How did you finally solved that? On Tuesday, October 24

May 3

张东, Yangkang Chen2

May 3

BSM analysis in parallel evolution

I'm also facing the same problem. Did you managed to solve that? On Monday, June 20, 2022 at 11:

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BSM analysis in parallel evolution

I'm also facing the same problem. Did you managed to solve that? On Monday, June 20, 2022 at 11:

May 3

May 3

Positively selected sites have no mutation

Hi all, I was using Branch-Site model (Model A vs. counterpart null model with w=1). I wish to see

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Positively selected sites have no mutation

Hi all, I was using Branch-Site model (Model A vs. counterpart null model with w=1). I wish to see

May 3

SOMNATH CHINDHE

Apr 25

Codon usage table

Hello Experts, I want to do pairwise dnds calculation using the yn00 program in paml. However, I want

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Codon usage table

Hello Experts, I want to do pairwise dnds calculation using the yn00 program in paml. However, I want

Apr 25

LysM LRR, Janet Young3

Apr 19

M7vsM8; LRT not significant; M8 found 9 sites

Dear Janet, Thank you for your kind reply. The information was really helpful. With greetings, Tanbir

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M7vsM8; LRT not significant; M8 found 9 sites

Dear Janet, Thank you for your kind reply. The information was really helpful. With greetings, Tanbir

Apr 19

Lala, Janet Young3

Apr 17

Error: end of tree file.. paml-4.10.6

Hi Janet, and thank you so much!! That was indeed the issue! And you are absolutely right I should

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Error: end of tree file.. paml-4.10.6

Hi Janet, and thank you so much!! That was indeed the issue! And you are absolutely right I should

Apr 17

Yuma, Sishuo Wang2

Apr 15

Hi Yuma, I guess you still need a tree, unless you use yn00 but yn00 is not for amino acid sequence.

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Hi Yuma, I guess you still need a tree, unless you use yn00 but yn00 is not for amino acid sequence.

Apr 15

Mar 11

Hi everyone, I'd like to apply a Clade modelC to detect positive selection in a certain lineages.

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Hi everyone, I'd like to apply a Clade modelC to detect positive selection in a certain lineages.

Mar 11

Maria Eduarda Lacerda, Janet Young2

Mar 6

Error: Seq # occurs more than once in the tree

hi, The error message might be telling you that the sequence NAME that occurs more than once rather

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Error: Seq # occurs more than once in the tree

hi, The error message might be telling you that the sequence NAME that occurs more than once rather

Mar 6

Feb 24

Multi-nucleotide substitutions

Growing body of evidence shows that multi-nucleotide substitutions can result in spurious detection

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Multi-nucleotide substitutions

Growing body of evidence shows that multi-nucleotide substitutions can result in spurious detection

Feb 24

Arthur Tugume, … Ziheng6

Feb 19

Why strong positive selection in short BUT strong negative selection in large protein

Yang Z, Lauder IJ, Lin HJ. 1995. Molecular evolution of the hepatitis B virus genome. J Mol Evol 41:

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Why strong positive selection in short BUT strong negative selection in large protein

Yang Z, Lauder IJ, Lin HJ. 1995. Molecular evolution of the hepatitis B virus genome. J Mol Evol 41:

Feb 19

kim.ve...@gmail.com, Ziheng2

Feb 19

free-ratio error fh=negative

omega=0 is not a valid value for the parameter so you should not use it as the initial value. the

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free-ratio error fh=negative

omega=0 is not a valid value for the parameter so you should not use it as the initial value. the

Feb 19

Joel Sharbrough, Ziheng2

Feb 19

How does model 0 work?

When I perform identical replicate runes using model 1 (free-ratio model) or model 2 (>1 ratio

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How does model 0 work?

When I perform identical replicate runes using model 1 (free-ratio model) or model 2 (>1 ratio

Feb 19

Feb 19

significant LRT but only 2a proportion is one

that looks like a very unusual gene. what's special about the data? ziheng On Sunday, 22 January

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significant LRT but only 2a proportion is one

that looks like a very unusual gene. what's special about the data? ziheng On Sunday, 22 January

Feb 19

Feb 19

branch-site models

i suggest that you find a few review papers on the topic. this is not really the right place for a

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branch-site models

i suggest that you find a few review papers on the topic. this is not really the right place for a

Feb 19

pan pan, Ziheng2

Feb 19

A running problem in codeml.Please help!!

you can separate the dataset into a different file, and run the program a few times to see whether it

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A running problem in codeml.Please help!!

you can separate the dataset into a different file, and run the program a few times to see whether it

Feb 19

Jeffrey Sosa-Calvo, Ziheng2

Feb 19

lnL error. Something is wrong in minB

the program is doing some error checking, but in this case the difference is small and is most likely

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lnL error. Something is wrong in minB

the program is doing some error checking, but in this case the difference is small and is most likely

Feb 19

Carin Tarasyan, Sandra AC3

Jan 13

Problem with PAMLX on Ubuntu 18

Thanks a lot for the answer! You are absolutely right: paml software is requires qt4 not the qt5,

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Problem with PAMLX on Ubuntu 18

Thanks a lot for the answer! You are absolutely right: paml software is requires qt4 not the qt5,

Jan 13

kim, Sandra AC3

Jan 6

Error: some gene labels are missing

Hi Sandra, Thank you for your response. I installed PAML v4.10.6 and re-ran the analysis, and got the

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Error: some gene labels are missing

Hi Sandra, Thank you for your response. I installed PAML v4.10.6 and re-ran the analysis, and got the

Jan 6

Avehi Singh, Janet Young3

12/19/22

Issues with input tree

Thank you so much! I changed the labels of the duplicate sequences and this worked! On Friday,

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Issues with input tree

Thank you so much! I changed the labels of the duplicate sequences and this worked! On Friday,

12/19/22

Boka, Sandra AC2

12/15/22

mcmctree - sigma2_gamma argument

Hi Boka, This option in the MCMCtree control file specifies the values of the alpha and beta

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mcmctree - sigma2_gamma argument

Hi Boka, This option in the MCMCtree control file specifies the values of the alpha and beta

12/15/22

sunny kevin, Sandra AC2

12/12/22

Hi Kevin, You should ignore the NEB a analysis and focus on the results output by the BEB analysis (

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Hi Kevin, You should ignore the NEB a analysis and focus on the results output by the BEB analysis (

12/12/22

FloraWF, Sandra AC2

12/12/22

Branch-site output analysis - ranking selection

Hi Flora, The information about estimated ω can be found here: MLEs of dN/dS (w) for site classes (K=

unread,

Branch-site output analysis - ranking selection

Hi Flora, The information about estimated ω can be found here: MLEs of dN/dS (w) for site classes (K=

12/12/22

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