PAML discussion group

1–30 of 909

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

Jan 23

Using data from many single copy orthologs to build single tree

Attached is a very small example dataset: 2 FASTA files containing the protein sequence for the 6

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Using data from many single copy orthologs to build single tree

Attached is a very small example dataset: 2 FASTA files containing the protein sequence for the 6

Jan 23

Jan 21

significant LRT but only 2a proportion is one

Hi All, When likelihood ratio test in branch-site analysis is significant and 2a proportion is 1

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significant LRT but only 2a proportion is one

Hi All, When likelihood ratio test in branch-site analysis is significant and 2a proportion is 1

Jan 21

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.ve...@gmail.com

Jan 11

free-ratio error fh=negative

Hi PAML group, I am running two-ratio (model=2, NSsites=0, fix_omega=0) and free-ratio (model=1,

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free-ratio error fh=negative

Hi PAML group, I am running two-ratio (model=2, NSsites=0, fix_omega=0) and free-ratio (model=1,

Jan 11

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

12/27/22

site class proportions

Hi All, I did a branch-site dN/dS test. One of the results for a gene shows that expect one all the

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site class proportions

Hi All, I did a branch-site dN/dS test. One of the results for a gene shows that expect one all the

12/27/22

12/27/22

site class proportions

Hi All, I did a branch-site dN/dS test. One of the results for a gene shows that expect one all the

unread,

site class proportions

Hi All, I did a branch-site dN/dS test. One of the results for a gene shows that expect one all the

12/27/22

Joel Sharbrough

12/20/22

How does model 0 work?

Hello, I am trying to better understand how model 0 (ie, one-ratio model) works in the branch models.

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How does model 0 work?

Hello, I am trying to better understand how model 0 (ie, one-ratio model) works in the branch models.

12/20/22

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

Arthur Tugume, … Janet Young5

12/15/22

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

hi Arthur, I noticed your original question says that the portion that's not detected in nature

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

hi Arthur, I noticed your original question says that the portion that's not detected in nature

12/15/22

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=

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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

Jui-Hung, Sandra AC2

12/12/22

Error: check and think about multifurcating trees..

Hi Jui-Hung, I have quickly opened your tree file with FigTree, and it seems that you had a

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Error: check and think about multifurcating trees..

Hi Jui-Hung, I have quickly opened your tree file with FigTree, and it seems that you had a

12/12/22

Camilo Parada Rojas, … Sandra AC4

12/12/22

dN/dS for each branch in tree! Please help

Hi Camilo, The trees that you use with CODEML cannot include branch lengths or bootstrap values: you

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dN/dS for each branch in tree! Please help

Hi Camilo, The trees that you use with CODEML cannot include branch lengths or bootstrap values: you

12/12/22

Abu Naser, Sandra AC2

12/12/22

not getting substitution rate from baseml

Hi Abu, Without knowing the options you have used in the control file or whether the input files have

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not getting substitution rate from baseml

Hi Abu, Without knowing the options you have used in the control file or whether the input files have

12/12/22

Jenna Gizzi, … Sandra AC4

12/12/22

Seqfile problem CodeML

Hi Jenna, You may want to check the following (some of the checks I detail below have already been

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Seqfile problem CodeML

Hi Jenna, You may want to check the following (some of the checks I detail below have already been

12/12/22

kashish kamra, Sandra AC2

12/12/22

Hi, The alignment file should be a codon alignment and in PHYLIP format, while the tree file should

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Hi, The alignment file should be a codon alignment and in PHYLIP format, while the tree file should

12/12/22

10/27/22

A running problem in codeml.Please help!!

Hello anyone There is a issue with running codeml，I use 13 datasets, running free-ratio model.When

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A running problem in codeml.Please help!!

Hello anyone There is a issue with running codeml，I use 13 datasets, running free-ratio model.When

10/27/22

Jeffrey Sosa-Calvo

10/6/22

lnL error. Something is wrong in minB

Hi Ziheng, Hope all is well. I am wondering about this error I just got while running MCMCTREE to

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lnL error. Something is wrong in minB

Hi Ziheng, Hope all is well. I am wondering about this error I just got while running MCMCTREE to

10/6/22

9/5/22

PAMP - shape parameter

How to find shape parameter using PAMP in PAML? What to put as input (tree and sequence)? and how to

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PAMP - shape parameter

How to find shape parameter using PAMP in PAML? What to put as input (tree and sequence)? and how to

9/5/22

7/22/22

Synonymous sites only for tree inference

perhaps you can use the 3rd codon positions. alternatively you can use the so called 4-fold

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Synonymous sites only for tree inference

perhaps you can use the 3rd codon positions. alternatively you can use the so called 4-fold

7/22/22

Fang Li, Ziheng2

7/22/22

mcmctree out of 95% confidence interval

that sounds strange. if you send me the files to reproduce the problem, i can have a look. please

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mcmctree out of 95% confidence interval

that sounds strange. if you send me the files to reproduce the problem, i can have a look. please

7/22/22

7/22/22

does it work if you try icode = 11 ziheng On Thursday, 16 June 2022 at 14:38:56 UTC+1 julia wrote: Hi

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does it work if you try icode = 11 ziheng On Thursday, 16 June 2022 at 14:38:56 UTC+1 julia wrote: Hi

7/22/22

张东, Ziheng2

7/22/22

interpretation of positive selected sites

the amino acid is the one from the first sequence in the alignment. also watch out for cleandata=1.

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interpretation of positive selected sites

the amino acid is the one from the first sequence in the alignment. also watch out for cleandata=1.

7/22/22

sunny kevin, Ziheng2

7/22/22

BEB and NEB Result

our recommendation is to ignore the NEB results and focus on the BEB results. in the output, there is

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BEB and NEB Result

our recommendation is to ignore the NEB results and focus on the BEB results. in the output, there is

7/22/22

Chenyu Fan, … Ziheng4

7/22/22

Question about total number of sites decreasing as the number of input sequences increasing

perhaps you are using the runmode = -2 option, which means pairwise comparison. with that option, the

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Question about total number of sites decreasing as the number of input sequences increasing

perhaps you are using the runmode = -2 option, which means pairwise comparison. with that option, the

7/22/22

sunny kevin, Ziheng2

7/22/22

Segmentation fault

there have been some recent changes to the ndata option. now the option assumes one tree from the

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Segmentation fault

there have been some recent changes to the ndata option. now the option assumes one tree from the

7/22/22

Chenyu Fan, Ziheng2

7/9/22

Total number of sites in codeml result doesn't match the number of the phylip file and '"42 columns are converted into ??? because of the stop codon TAA'

yes, you should delete stop codons. ziheng On Saturday, 2 July 2022 at 07:56:34 UTC+1 cheny...@

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Total number of sites in codeml result doesn't match the number of the phylip file and '"42 columns are converted into ??? because of the stop codon TAA'

yes, you should delete stop codons. ziheng On Saturday, 2 July 2022 at 07:56:34 UTC+1 cheny...@

7/9/22

Hu Ling, Ziheng2

7/9/22

look at some example sequence data files, and edit your file so that it has the right format. also

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look at some example sequence data files, and edit your file so that it has the right format. also

7/9/22

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