PAML discussion group

Contact owners and managers

1–30 of 973

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

Maryrose Kriegh

12:47 AM

Stranded Deep Alpha V0.24.01 PC

Stranded Deep Alpha v0.24.01 PC: A Survival Adventure Game Stranded Deep is a survival adventure game

unread,

Stranded Deep Alpha V0.24.01 PC

Stranded Deep Alpha v0.24.01 PC: A Survival Adventure Game Stranded Deep is a survival adventure game

12:47 AM

Maryrose Kriegh

12:47 AM

Giusti Santochi Tecnologia Meccanica E Studi Di Fabbricazione Torrent

Giusti Santochi Tecnologia Meccanica E Studi Di Fabbricazione Torrent: Scarica Il Libro Che Ti Spiega

unread,

Giusti Santochi Tecnologia Meccanica E Studi Di Fabbricazione Torrent

Giusti Santochi Tecnologia Meccanica E Studi Di Fabbricazione Torrent: Scarica Il Libro Che Ti Spiega

12:47 AM

Maryrose Kriegh

12:47 AM

Excel Community Medicine.pdfl

Excel Community Medicine.pdf: A Review of the 13th Edition If you are looking for a comprehensive and

unread,

Excel Community Medicine.pdfl

Excel Community Medicine.pdf: A Review of the 13th Edition If you are looking for a comprehensive and

12:47 AM

Maryrose Kriegh

Dec 8

DiskGetor-Data-Recovery-3.2.8-Software- -Serial-Key

DiskGetor-Data-Recovery-3.2.8-Software- -Serial-Key: How to Recover Your Lost Data for Free Have you

unread,

DiskGetor-Data-Recovery-3.2.8-Software- -Serial-Key

DiskGetor-Data-Recovery-3.2.8-Software- -Serial-Key: How to Recover Your Lost Data for Free Have you

Dec 8

Владимир Галимов

Dec 8

Web Game Vua Hai Tac Trung Quoc

Ở Trung Quốc, tựa game mobile mới của NetEase là Âm Dương Sư đã ra mắt ở vị trí thứ 4 trên bảng xếp

unread,

Web Game Vua Hai Tac Trung Quoc

Ở Trung Quốc, tựa game mobile mới của NetEase là Âm Dương Sư đã ra mắt ở vị trí thứ 4 trên bảng xếp

Dec 8

Владимир Галимов

Dec 8

Free Download Iromusic 2 For Android

free download iromusic 2 for android\nDownload https://t.co/0PaQVJghMy\n\n\n\n eebf2c3492\n\n\n

unread,

Free Download Iromusic 2 For Android

free download iromusic 2 for android\nDownload https://t.co/0PaQVJghMy\n\n\n\n eebf2c3492\n\n\n

Dec 8

Dec 7

Ashampoo Photo Optimizer 7.0.1.2 Crack [CracksMind] Full Version

Ashampoo Photo Optimizer 7.0.1.2 Crack [CracksMind] full version DOWNLOAD https://bltlly.com/2wITHs

unread,

Ashampoo Photo Optimizer 7.0.1.2 Crack [CracksMind] Full Version

Ashampoo Photo Optimizer 7.0.1.2 Crack [CracksMind] full version DOWNLOAD https://bltlly.com/2wITHs

Dec 7

Владимир Галимов

Dec 6

Suicide Commando Torrents

V-19 fighters were then deployed during the Battle of Teth, where Kenobi arrived with reinforcements

unread,

Suicide Commando Torrents

V-19 fighters were then deployed during the Battle of Teth, where Kenobi arrived with reinforcements

Dec 6

Dec 4

Color Correction Handbook Professional Techniques For Video And Cinema Pdf Download

Color Correction Handbook Professional Techniques For Video And Cinema Pdf Download Download File

unread,

Color Correction Handbook Professional Techniques For Video And Cinema Pdf Download

Color Correction Handbook Professional Techniques For Video And Cinema Pdf Download Download File

Dec 4

Dec 4

C Programming Ebook Pdf Free Download

Online PDF and eBooks will help you learn C right from the beginning section. In some of the eBooks,

unread,

C Programming Ebook Pdf Free Download

Online PDF and eBooks will help you learn C right from the beginning section. In some of the eBooks,

Dec 4

Dec 4

DIGIPERSON: A Socio-Technological Odyssey Books Pdf File

DIGIPERSON: A Socio-Technological Odyssey books pdf file Download Zip https://t.co/6UuBTjCIcV

unread,

DIGIPERSON: A Socio-Technological Odyssey Books Pdf File

DIGIPERSON: A Socio-Technological Odyssey books pdf file Download Zip https://t.co/6UuBTjCIcV

Dec 4

Dec 4

Sketchup Pro 2016 Crack File 12

sketchup pro 2016 crack file 12 Download https://t.co/gLxtm2dS51 eebf2c3492

unread,

Sketchup Pro 2016 Crack File 12

sketchup pro 2016 crack file 12 Download https://t.co/gLxtm2dS51 eebf2c3492

Dec 4

Sebastin Raveendar, Janet Young2

Nov 30

Error in tree and phylip alignment file

hi Sebastin, Your tree file looks strange - I think it contains 20 trees (and therefore KR078314 is

unread,

Error in tree and phylip alignment file

hi Sebastin, Your tree file looks strange - I think it contains 20 trees (and therefore KR078314 is

Nov 30

Olusola Akintayo Ogunyewo, Janet Young2

Nov 29

Error: not a multiple of 3!

Hi Olusola, How did you make the alignments? Make sure you use a reading-frame aware method. I notice

unread,

Error: not a multiple of 3!

Hi Olusola, How did you make the alignments? Make sure you use a reading-frame aware method. I notice

Nov 29

Nov 27

HD Online Player (velai Illa Pattathari Full Movie Dow)

How to Watch Velai Illa Pattathari Full Movie Online in HD QualityVelai Illa Pattathari (VIP) is a

unread,

HD Online Player (velai Illa Pattathari Full Movie Dow)

How to Watch Velai Illa Pattathari Full Movie Online in HD QualityVelai Illa Pattathari (VIP) is a

Nov 27

Nov 27

23 Jump Street Full Movie Subtitle Indonesia Download

How to Watch 23 Jump Street Full Movie with Subtitles in IndonesiaIf you are a fan of the comedy

unread,

23 Jump Street Full Movie Subtitle Indonesia Download

How to Watch 23 Jump Street Full Movie with Subtitles in IndonesiaIf you are a fan of the comedy

Nov 27

Olusola Akintayo Ogunyewo, Sishuo Wang2

Nov 27

Error: not a multiple of 3!

Hi Olusola, Would u pls mind providing the input and the ctrl file so that others can have a double

unread,

Error: not a multiple of 3!

Hi Olusola, Would u pls mind providing the input and the ctrl file so that others can have a double

Nov 27

bucek...@gmail.com, Sandra AC2

Nov 15

stdout of mcmctree - interpretation of values

Hi there, While you are running `MCMCtree` with `usedata = 3`, just wanted to clarify that the stage

unread,

stdout of mcmctree - interpretation of values

Hi there, While you are running `MCMCtree` with `usedata = 3`, just wanted to clarify that the stage

Nov 15

Lin Rikka, Sandra AC2

Nov 15

Error in sequence data file

Hi there! Not exactly sure about what issue you may be experiencing as you did not provide us with

unread,

Error in sequence data file

Hi there! Not exactly sure about what issue you may be experiencing as you did not provide us with

Nov 15

Vinciane Mossion, … Sandra AC18

Oct 26

codeML - Analyses with more than one gene stopped without error message

Hi Vinciane, I was thinking that you could submit a job array so that each alignment is analysed in

unread,

codeML - Analyses with more than one gene stopped without error message

Hi Vinciane, I was thinking that you could submit a job array so that each alignment is analysed in

Oct 26

Valeria RC, Sandra AC2

Oct 24

Error: Seq/species #X [name] occurs more than once in the tree

Hi there! I have not been able to reproduce your error with the latest PAML version. Which is the

unread,

Error: Seq/species #X [name] occurs more than once in the tree

Hi there! I have not been able to reproduce your error with the latest PAML version. Which is the

Oct 24

bucek...@gmail.com, Sandra AC5

Oct 22

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

Hi Ales, All the info regarding `MCMCtree` settings (as well as about other PAML programs settings)

unread,

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

Hi Ales, All the info regarding `MCMCtree` settings (as well as about other PAML programs settings)

Oct 22

Edyane Moraes, Sandra AC2

Oct 19

Hi there! You shall find many in-house scripts that can do this task, which also vary on your input

unread,

Hi there! You shall find many in-house scripts that can do this task, which also vary on your input

Oct 19

Amber Nashoba, Sishuo Wang3

Oct 11

dNdS, parameters: codeml sites model

sorry, the following is wrong: "the integral of a beta pdf in pamls" it should be corrected

unread,

dNdS, parameters: codeml sites model

sorry, the following is wrong: "the integral of a beta pdf in pamls" it should be corrected

Oct 11

Kelly, Sandra AC3

Oct 11

Error: maintree file can have only one tree.

Whoops, I think I sent that as a PM by accident. Let me know if you didn't get it, Sandra. And

unread,

Error: maintree file can have only one tree.

Whoops, I think I sent that as a PM by accident. Let me know if you didn't get it, Sandra. And

Oct 11

Keith Harrison, Sandra AC2

Oct 4

PamlX Stuck on start screen

Hi there! As far as I am concerned, pamlX is not maintained anymore and some of these issues might be

unread,

PamlX Stuck on start screen

Hi there! As far as I am concerned, pamlX is not maintained anymore and some of these issues might be

Oct 4

Romina Batista, Sandra AC8

Sep 21

paml-tutorial/positive-selection/02_extra_analyses/case_c

Hi Romina, Great to see that two problems have now been sorted! With regards to your last concern, I

unread,

paml-tutorial/positive-selection/02_extra_analyses/case_c

Hi Romina, Great to see that two problems have now been sorted! With regards to your last concern, I

Sep 21

Jingliang Kang, Sishuo Wang2

Sep 20

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

i am unsure if codeml allows estimating the frequency so u can use iqtree +g+f or raxml +g+f0 or +g+

unread,

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

i am unsure if codeml allows estimating the frequency so u can use iqtree +g+f or raxml +g+f0 or +g+

Sep 20

Rishabh Kapoor, Sishuo Wang2

Sep 19

LRT for evaluating selective restraint

Hi there, I think that it sounds reasonable. Or perhaps more specifically, it implies no selective

unread,

LRT for evaluating selective restraint

Hi there, I think that it sounds reasonable. Or perhaps more specifically, it implies no selective

Sep 19

André Santos, Sishuo Wang2

Sep 19

MCMCTree outputs time units are not in million years.

Hi André, I don't thin ur doing anything wrong. i think this is related to how to display them in

unread,

MCMCTree outputs time units are not in million years.

Hi André, I don't thin ur doing anything wrong. i think this is related to how to display them in

Sep 19

Search

Clear search

Close search

Google apps

Main menu