raxml

1–30 of 2070

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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Diego Soto Arancibia, Alexandros Stamatakis2

Sep 10

Guide tree for correcting topology

Dear Diego, > Hi everyone! I'm trying to become independent from CIPRES haha and learn > to

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Guide tree for correcting topology

Dear Diego, > Hi everyone! I'm trying to become independent from CIPRES haha and learn > to

Sep 10

Diego Soto Arancibia

Sep 9

Help with adding partitions and a guidetree for raxml inference

Hi everyone! I'm trying to become independent from CIPRES haha and give it a try to the manual

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Help with adding partitions and a guidetree for raxml inference

Hi everyone! I'm trying to become independent from CIPRES haha and give it a try to the manual

Sep 9

Wayne Pfeiffer, Oleksiy Kozlov4

Sep 2

Long time to finish convergence

Hi Oleksiy, Both of your suggestions speeded up the time to converge :) For the most part this led to

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Long time to finish convergence

Hi Oleksiy, Both of your suggestions speeded up the time to converge :) For the most part this led to

Sep 2

Alexandros Stamatakis

Sep 1

Machine Learning for Evolutionary Genomics (Legend2025) abstract submission deadline: September 2022

Dear Users of our SW tools, Do you want to spend time in the French Alps and talk about Machine

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Machine Learning for Evolutionary Genomics (Legend2025) abstract submission deadline: September 2022

Dear Users of our SW tools, Do you want to spend time in the French Alps and talk about Machine

Sep 1

Kevin Myers, Anastasis Togkousidis3

Aug 19

RAxML-ng adaptive segmentation fault on Linux

Thanks Anastasis! We will try the beta version on our cluster and see how that works. I will reply

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RAxML-ng adaptive segmentation fault on Linux

Thanks Anastasis! We will try the beta version on our cluster and see how that works. I will reply

Aug 19

anwesha mimi Saha, Benoit Morel2

Aug 2

Pargenes-export / ASTRAL / ASTER

Hello, The easiest way to run Astral is to run your gene tree inferences with pargenes, but add

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Pargenes-export / ASTRAL / ASTER

Hello, The easiest way to run Astral is to run your gene tree inferences with pargenes, but add

Aug 2

anwesha mimi Saha, Benoit Morel3

Jul 24

Pargenes output :mlsearch_run; bootstraps; support_runs folder output empty.

Thanks, now I can open the files :-) I'm not quite sure yet, but I suspect that there is a space

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Pargenes output :mlsearch_run; bootstraps; support_runs folder output empty.

Thanks, now I can open the files :-) I'm not quite sure yet, but I suspect that there is a space

Jul 24

Črt Pantner, … J Hengstler7

Jul 23

Number of free parameters vs alignment size

> which makes sense since RAxML-ng automatically removes duplicates No, raxml does not do that. It

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Number of free parameters vs alignment size

> which makes sense since RAxML-ng automatically removes duplicates No, raxml does not do that. It

Jul 23

Van Nguyen, Oleksiy Kozlov2

Jul 7

Diploid genotypes rates for double substitutions

Dear Van, thanks for reporting, and sorry for the late reply, I had to find time to dig into this old

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Diploid genotypes rates for double substitutions

Dear Van, thanks for reporting, and sorry for the late reply, I had to find time to dig into this old

Jul 7

Austin Chipps, Oleksiy Kozlov2

Jun 25

Internode certainty

Hi Austin, IC/ICA and other advanced support metrics are implemented in raxml-ng 2.0, which is

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Internode certainty

Hi Austin, IC/ICA and other advanced support metrics are implemented in raxml-ng 2.0, which is

Jun 25

Paweł Olszewski, Oleksiy Kozlov2

Jun 24

Log file

Hi Paweł, since you are apparently running raxml-ng from withn WSL, you should fix MSA path like this

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Log file

Hi Paweł, since you are apparently running raxml-ng from withn WSL, you should fix MSA path like this

Jun 24

Alexandros Stamatakis

Jun 18

2nd Conference on Machine Learning for Evolutionary Genomics - French Alps

Dear Users of our Software Tools, Do you fancy spending some days in the French Alps in December and

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2nd Conference on Machine Learning for Evolutionary Genomics - French Alps

Dear Users of our Software Tools, Do you fancy spending some days in the French Alps in December and

Jun 18

Scarivanny, … Oleksiy Kozlov4

May 28

RAxML Error

Dear Sofia, this seems to be a problem with modeltest-ng, so please ask your question in the

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RAxML Error

Dear Sofia, this seems to be a problem with modeltest-ng, so please ask your question in the

May 28

Alexandros Stamatakis

May 15

RAxML-NG v2.0 beta

Dear Users, We are happy to announce the release of RAxML-NG v2.0 beta https://github.com/amkozlov/

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RAxML-NG v2.0 beta

Dear Users, We are happy to announce the release of RAxML-NG v2.0 beta https://github.com/amkozlov/

May 15

Rachel Isaac, Oleksiy Kozlov3

May 14

Speed Issue when using a university Cluster

Hi Rachel, since you are apparently not using MPI, you should set #SBATCH --ntasks=1 #SBATCH --hint=

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Speed Issue when using a university Cluster

Hi Rachel, since you are apparently not using MPI, you should set #SBATCH --ntasks=1 #SBATCH --hint=

May 14

david ferreiro garcia, … Hengstler, Johannes4

Apr 30

RAxML Compatibility with 3Di Character Alignments and Likelihood Comparability

Hi David, I might have been wrong on the comparability. We tried to get phylogenic inference working

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RAxML Compatibility with 3Di Character Alignments and Likelihood Comparability

Hi David, I might have been wrong on the comparability. We tried to get phylogenic inference working

Apr 30

xiaoyu zhao, Alexandros Stamatakis2

Apr 24

Can I Map Bootstrap to Separately Generated ML Tree?

Dear Xiaoyu, This will be perfectly fine, both scientifically and in terms of expected quality of

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Can I Map Bootstrap to Separately Generated ML Tree?

Dear Xiaoyu, This will be perfectly fine, both scientifically and in terms of expected quality of

Apr 24

Ezra Bailey, … Oleksiy Kozlov8

Apr 9

Partitioning only 2nd and 1st+2nd codon positions

Hi again, Using RAxML-NG locally and adjusting my partition file to use as the --model worked

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Partitioning only 2nd and 1st+2nd codon positions

Hi again, Using RAxML-NG locally and adjusting my partition file to use as the --model worked

Apr 9

Vân Nguyễn, … Bui Quang Minh8

Mar 27

RNA models and bootstrap values of trees inferred with RNA models

Hi Alexis, Thank you for the confirmation! I agree, better have an additional tool to prepare input

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RNA models and bootstrap values of trees inferred with RNA models

Hi Alexis, Thank you for the confirmation! I agree, better have an additional tool to prepare input

Mar 27

Alexandros Stamatakis

Mar 26

Workshop on Biodiversity Genomics in Crete - May 2025

Dear Users of our software tools, Are you looking for a good excuse to visit Crete? Join us for the

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Workshop on Biodiversity Genomics in Crete - May 2025

Dear Users of our software tools, Are you looking for a good excuse to visit Crete? Join us for the

Mar 26

Kenta Renard, Oleksiy Kozlov2

Mar 19

Mixture model PAML format input

Dear Kenta, user-defined mixture models are not supported by RAxML-NG as of now, sorry. Best, Oleksiy

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Mixture model PAML format input

Dear Kenta, user-defined mixture models are not supported by RAxML-NG as of now, sorry. Best, Oleksiy

Mar 19

Alexandros Stamatakis

Mar 19

raxtax: a novel tool for taxonomic classification

Dear Users Check out raxtax, our new open-source tool for taxonomic classification of barcoding

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raxtax: a novel tool for taxonomic classification

Dear Users Check out raxtax, our new open-source tool for taxonomic classification of barcoding

Mar 19

rutge...@naturalis.nl, Alexandros Stamatakis3

Mar 16

RAxML EPA expectation management

Dear Alexis, how nice to hear from you! I am very well, thank you - hope you are too. Indeed, I

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RAxML EPA expectation management

Dear Alexis, how nice to hear from you! I am very well, thank you - hope you are too. Indeed, I

Mar 16

Alexandros Stamatakis

Feb 24

LEGEND conference on Machine Learning for Evolutionary Genomics Data - French Alps - Dec 8-12 2025

Dear Users of our tools, The second edition of our LEGEND conference on Machine Learning for

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LEGEND conference on Machine Learning for Evolutionary Genomics Data - French Alps - Dec 8-12 2025

Dear Users of our tools, The second edition of our LEGEND conference on Machine Learning for

Feb 24

Daniel Lundin

Feb 22

nf-core/phyloplace 2.0.0 released

Hi everyone, Two years after the first release of nf-core/phyloplace, I released 2.0.0 today. Docs

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nf-core/phyloplace 2.0.0 released

Hi everyone, Two years after the first release of nf-core/phyloplace, I released 2.0.0 today. Docs

Feb 22

Kenta Renard, Oleksiy Kozlov3

Feb 18

Log file issues when resuming from checkpoint

Dear Kenta, sorry for the late response, and thanks for sending the files! This is indeed a bug in

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Log file issues when resuming from checkpoint

Dear Kenta, sorry for the late response, and thanks for sending the files! This is indeed a bug in

Feb 18

Agnès Baud, Oleksiy Kozlov2

Feb 17

RAxML-NG: ERROR: vector::_M_default_append

Hi Agnès, you used a newer raxml-ng version for the 2nd run (1.2.2), which failed to load a

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RAxML-NG: ERROR: vector::_M_default_append

Hi Agnès, you used a newer raxml-ng version for the 2nd run (1.2.2), which failed to load a

Feb 17

Mariana Meneguzzi, … Grimm5

Feb 14

Pairwise distance matrix from RAxML?

"Matrix.epf" is just a placeholder name for the MSA. You of course have to read in your

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Pairwise distance matrix from RAxML?

"Matrix.epf" is just a placeholder name for the MSA. You of course have to read in your

Feb 14

Kenta Renard, … Anastasis Togkousidis3

Feb 7

RAxML-NG 2 (dev version) questions

Dear Kenta, If you intend to publish any results inferred from the current adaptive heuristic in

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RAxML-NG 2 (dev version) questions

Dear Kenta, If you intend to publish any results inferred from the current adaptive heuristic in

Feb 7

Alejandro Petroni, … Grimm4

Feb 5

Best command to run RAxML-NG for a large alignment

Hi Alejandro, why do you need bootstrap support at all, when your objective is "just to get a

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Best command to run RAxML-NG for a large alignment

Hi Alejandro, why do you need bootstrap support at all, when your objective is "just to get a

Feb 5