raxml

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This group is for asking question concerning RAxML-NG, RAxML, RAxML-Light, RAxML-EPA, PaPaRa, and ParGenes.

Please use the search function prior to posting questions, since most of the typical questions have already been answered in here.

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Nick

3:44 PM

mpi error

I got the following error when running raxml-ng-mpi: ------------------------------------------------

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mpi error

I got the following error when running raxml-ng-mpi: ------------------------------------------------

3:44 PM

Nick, Alexey Kozlov2

Sep 29

raxml-ng-mpi job not checkpointing

Hi Nick, please if possible upgrade to the latest version (1.1.0) and re-run with "--log debug

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raxml-ng-mpi job not checkpointing

Hi Nick, please if possible upgrade to the latest version (1.1.0) and re-run with "--log debug

Sep 29

Alexandros Stamatakis, Florinda D'Archivio3

Sep 29

Re: [raxml] boot strap

The small branch lengths could be part of what you are observing for sure. Are those very closely

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Re: [raxml] boot strap

The small branch lengths could be part of what you are observing for sure. Are those very closely

Sep 29

Berkay SELÇUK, … Grimm5

Sep 29

Suggestions for multi-gene tree construction

Merhaba Berkay, Re first question: In principle, yes. Using reduced-tip, ie partial trees, and map

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Suggestions for multi-gene tree construction

Merhaba Berkay, Re first question: In principle, yes. Using reduced-tip, ie partial trees, and map

Sep 29

Chahat Upreti, Alexandros Stamatakis5

Sep 28

Should assemblies be removed if core gene alignment shows redundancies?

Thanks so much! On Tuesday, September 27, 2022 at 1:32:17 AM UTC-5 Alexis wrote: Dear Chahat, >

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Should assemblies be removed if core gene alignment shows redundancies?

Thanks so much! On Tuesday, September 27, 2022 at 1:32:17 AM UTC-5 Alexis wrote: Dear Chahat, >

Sep 28

Sheila Rodríguez Machado, … Alexey Kozlov6

Sep 24

RAxML partition file format error in CIPRES

Thank y'all for your answers! Have a great weekend. Will let you know if it works. Best, Sheila

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RAxML partition file format error in CIPRES

Thank y'all for your answers! Have a great weekend. Will let you know if it works. Best, Sheila

Sep 24

Vanessa Bieker, … Guido12

Sep 23

Ancestral state estimate - undetermined columns

Hi Vanessa, > > Thanks a lot for your detailed explanation! My background is in > population

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Ancestral state estimate - undetermined columns

Hi Vanessa, > > Thanks a lot for your detailed explanation! My background is in > population

Sep 23

Alexey Kozlov

Sep 21

Re: [raxml] raxml-ng in the GUI version

Dear Florinda, please contact the developers of raxmlGUI: raxmlgui.help@gmail.com https://github.com/

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Re: [raxml] raxml-ng in the GUI version

Dear Florinda, please contact the developers of raxmlGUI: raxmlgui.help@gmail.com https://github.com/

Sep 21

Pablo V, … Alexandros Stamatakis6

Sep 16

Tried running ML with 100 bootstrap and obtained a cladogram

Dear Pablo, > Thanks a lot for the advice Alexis!!!! It has worked perfectly. I mapped > the

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Tried running ML with 100 bootstrap and obtained a cladogram

Dear Pablo, > Thanks a lot for the advice Alexis!!!! It has worked perfectly. I mapped > the

Sep 16

krishna acharya, … Pfeiffer, Wayne3

Sep 15

Why raxml is taking is too long to generate raxml tree

Hi Krishna, If you have not gotten your RAxML analysis to complete expeditiously, you could try the

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Why raxml is taking is too long to generate raxml tree

Hi Krishna, If you have not gotten your RAxML analysis to complete expeditiously, you could try the

Sep 15

Alexandros Stamatakis, Grimm2

Sep 14

Re: [raxml] substitution model

Hi Florinda, to be on the really safe side, and if feasible (time-wise), make three inferences. One

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Re: [raxml] substitution model

Hi Florinda, to be on the really safe side, and if feasible (time-wise), make three inferences. One

Sep 14

Alexandros Stamatakis, … Norbert5

Sep 14

NetRAX software for Maximum Likelihood based inference of phylogenetic networks

Dear Norbert, The installtion should work on any Linux-based system as long as cmake, git, gcc and

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NetRAX software for Maximum Likelihood based inference of phylogenetic networks

Dear Norbert, The installtion should work on any Linux-based system as long as cmake, git, gcc and

Sep 14

EB Wong, Alexey Kozlov2

Sep 12

Model Partition in RAxML-NG Tree Calculation

Hi, combining multiple genes with the same substitution model into a single partition would result in

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Model Partition in RAxML-NG Tree Calculation

Hi, combining multiple genes with the same substitution model into a single partition would result in

Sep 12

Alexandros Stamatakis2

Sep 12

Applications for 2023 school on Computational Molecular Evolution are open

Here is a reminder, applications for our summer school will close on November 1st 2022. Alexis On

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Applications for 2023 school on Computational Molecular Evolution are open

Here is a reminder, applications for our summer school will close on November 1st 2022. Alexis On

Sep 12

EB Wong, Alexey Kozlov2

Sep 5

Differences in the released of the same RAxML-NG version

Hello, when you clone raxml-ng repository from github, you get the latest version with updates made

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Differences in the released of the same RAxML-NG version

Hello, when you clone raxml-ng repository from github, you get the latest version with updates made

Sep 5

ANA CARLOTA GRACIA SANCHA, Alexandros Stamatakis2

Sep 5

RaxmlGUI2 encountered an error

Please contact the developers of RAxML GUI 2, this GUI was not developed by us and we do hence not

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RaxmlGUI2 encountered an error

Please contact the developers of RAxML GUI 2, this GUI was not developed by us and we do hence not

Sep 5

Wai Yan Choi, … Victor Lin8

Sep 2

Problem on compiling RAxML (make -f Makefile.gcc)

I was able to compile on an M1 mac with a few changes. This should work: git clone --recurse-

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Problem on compiling RAxML (make -f Makefile.gcc)

I was able to compile on an M1 mac with a few changes. This should work: git clone --recurse-

Sep 2

Ketaki Hardikar, … Harsh Kashyap3

Sep 1

GTR+gamma

Please check for GTR in Detail On Thursday, 1 September, 2022 at 12:23:19 am UTC+5:30 hardika...@

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GTR+gamma

Please check for GTR in Detail On Thursday, 1 September, 2022 at 12:23:19 am UTC+5:30 hardika...@

Sep 1

jj biodiversity, … Grimm18

Aug 29

Monophyletic... or?

Hi Jeong, just a little thing you may want to check (if possible with your data) regarding your

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Monophyletic... or?

Hi Jeong, just a little thing you may want to check (if possible with your data) regarding your

Aug 29

Nick, Alexandros Stamatakis2

Aug 22

ambiguous characters in raxml-ng

they are all being treated the same as undetermined characters (in fact this holds true for the vast

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ambiguous characters in raxml-ng

they are all being treated the same as undetermined characters (in fact this holds true for the vast

Aug 22

NEELAM KUSHWAHA, Alexandros Stamatakis2

Aug 17

Problem reading alignment file

the problem seems to be the space between: CP028959.1_4930 and P_aeruginosa_IMP66resi try inserting

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Problem reading alignment file

the problem seems to be the space between: CP028959.1_4930 and P_aeruginosa_IMP66resi try inserting

Aug 17

Pablo V, Alexandros Stamatakis2

Aug 16

problem with memory

At: https://cme.h-its.org/exelixis/web/software/raxml/index.html there is a little web form for

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problem with memory

At: https://cme.h-its.org/exelixis/web/software/raxml/index.html there is a little web form for

Aug 16

Ketaki Hardikar, Alexandros Stamatakis2

Aug 16

raxml ML+rapid bootstrap tree output differences

best tree: best found ML tree bipartitions tree: best found ML tree with bootstrap supports On 15.08.

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raxml ML+rapid bootstrap tree output differences

best tree: best found ML tree bipartitions tree: best found ML tree with bootstrap supports On 15.08.

Aug 16

Daryl Lam, Alexandros Stamatakis2

Aug 5

Issue using RaxML-ng to make an ExaBayes consensus tree

Dear Daryl, Thanks, could you maybe send us a small sample of the trees (to a personal email if you

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Issue using RaxML-ng to make an ExaBayes consensus tree

Dear Daryl, Thanks, could you maybe send us a small sample of the trees (to a personal email if you

Aug 5

Alexandros Stamatakis, … Pfeiffer, Wayne8

Jul 28

A free performance lunch for ML inference

Hi Alexis, In response to your comment, I executed the tree evaluation option with the original code

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A free performance lunch for ML inference

Hi Alexis, In response to your comment, I executed the tree evaluation option with the original code

Jul 28

Brandon Stark, Alexandros Stamatakis4

Jul 17

how to compare the topology similarity between full tree and subsampled trees?

What exactly are you not able to find? Alexis On 17.07.22 06:58, Brandon Stark wrote: > sorry, i

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how to compare the topology similarity between full tree and subsampled trees?

What exactly are you not able to find? Alexis On 17.07.22 06:58, Brandon Stark wrote: > sorry, i

Jul 17

Hiren Ghosh, … Alexandros Stamatakis6

Jul 11

RaxMl error "non-whitespace characters!" at end

Hi Stefany, First of all please use the new version of RAxML-NG (https://github.com/amkozlov/raxml-ng

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RaxMl error "non-whitespace characters!" at end

Hi Stefany, First of all please use the new version of RAxML-NG (https://github.com/amkozlov/raxml-ng

Jul 11

Nick, Alexandros Stamatakis4

Jul 6

Killed job, how to compute branch support

> I do not see the equivalent files in my output. These are the files I have: > >

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Killed job, how to compute branch support

> I do not see the equivalent files in my output. These are the files I have: > >

Jul 6

Joker Leo, Grimm2

Jul 1

RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file

Hi jk_..., this just means your MSA has the wrong input format. Please check the manual for

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RAxML can't, parse the alignment file as phylip file it will now try to parse it as FASTA file

Hi jk_..., this just means your MSA has the wrong input format. Please check the manual for

Jul 1

Anubha Pathak, Alexandros Stamatakis2

Jun 26

HKY+G model in RaxmlGUI2.0

We are not the developers of the RAxML-GUI, we have developed RAxML on which the GUI is based, so we

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HKY+G model in RaxmlGUI2.0

We are not the developers of the RAxML-GUI, we have developed RAxML on which the GUI is based, so we

Jun 26