raxml

1–30 of 2078

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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Stepan Puhov, … Kenta Renard11

Jan 1

Support for site-specific frequency profiles

Hi Stepan, I came across this because I really want to implement empirical profile mixture models (or

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Support for site-specific frequency profiles

Hi Stepan, I came across this because I really want to implement empirical profile mixture models (or

Jan 1

Oleksiy Kozlov

12/24/25

RAxML-NG is now available in Galaxy

Dear all, I'm happy to announce that RAxML-NG (v. 1.2.2) is now integrated into the Galaxy

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RAxML-NG is now available in Galaxy

Dear all, I'm happy to announce that RAxML-NG (v. 1.2.2) is now integrated into the Galaxy

12/24/25

Vân Nguyễn, … Daniel L9

12/20/25

RNA models and bootstrap values of trees inferred with RNA models

Dear Alexis, (and anyone that can help) I saw your reply: "...discussed this with Alexey

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RNA models and bootstrap values of trees inferred with RNA models

Dear Alexis, (and anyone that can help) I saw your reply: "...discussed this with Alexey

12/20/25

Alexandros Stamatakis

12/17/25

raxtax: a new fast and scalable taxonomic classifier

Dear Users, Our new raxtax tool for taxonomic classification is now published and available for use.

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raxtax: a new fast and scalable taxonomic classifier

Dear Users, Our new raxtax tool for taxonomic classification is now published and available for use.

12/17/25

Alexandros Stamatakis

12/15/25

Permanent Research Group Leader Position, Crete, Greece: Biodiversity Computing

Dear All, There is a permanent research group leader position available in Crete, Greece. The

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Permanent Research Group Leader Position, Crete, Greece: Biodiversity Computing

Dear All, There is a permanent research group leader position available in Crete, Greece. The

12/15/25

Alexandros Stamatakis

12/5/25

May 2026 Crete, Greece: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

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May 2026 Crete, Greece: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

12/5/25

Alexandros Stamatakis

11/3/25

Crete, Greece, May 2026: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

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Crete, Greece, May 2026: Mathematical and Computational Evolutionary Biology Meeting

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

11/3/25

Alexandros Stamatakis

11/3/25

Crete, Greece:

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

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Crete, Greece:

Dear Users of our Tools, Please consider joining us in Crete in May 2026 for the annual instance of

11/3/25

Alexandros Stamatakis

10/13/25

Dear Users of our SW tools, October 17 is your last chance to register for the 2nd conference on

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Dear Users of our SW tools, October 17 is your last chance to register for the 2nd conference on

10/13/25

David Iglesias, … Oleksiy Kozlov6

10/3/25

Links broken in the page

Thanks so much! On Thu, Oct 2, 2025 at 7:00 AM Oleksiy Kozlov <alexei...@gmail.com> wrote:

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Links broken in the page

Thanks so much! On Thu, Oct 2, 2025 at 7:00 AM Oleksiy Kozlov <alexei...@gmail.com> wrote:

10/3/25

Diego Soto Arancibia, Alexandros Stamatakis2

9/10/25

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

9/10/25

Diego Soto Arancibia

9/9/25

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

9/9/25

Wayne Pfeiffer, Oleksiy Kozlov4

9/2/25

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

9/2/25

Alexandros Stamatakis

9/1/25

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

9/1/25

Kevin Myers, Anastasis Togkousidis3

8/19/25

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

8/19/25

anwesha mimi Saha, Benoit Morel2

8/2/25

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

8/2/25

anwesha mimi Saha, Benoit Morel3

7/24/25

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

7/24/25

Črt Pantner, … J Hengstler7

7/23/25

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

7/23/25

Van Nguyen, Oleksiy Kozlov2

7/7/25

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

7/7/25

Austin Chipps, Oleksiy Kozlov2

6/25/25

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

6/25/25

Paweł Olszewski, Oleksiy Kozlov2

6/24/25

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

6/24/25

Alexandros Stamatakis

6/18/25

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

6/18/25

Scarivanny, … Oleksiy Kozlov4

5/28/25

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

5/28/25

Alexandros Stamatakis

5/15/25

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/

5/15/25

Rachel Isaac, Oleksiy Kozlov3

5/14/25

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=

5/14/25

david ferreiro garcia, … Hengstler, Johannes4

4/30/25

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

4/30/25

xiaoyu zhao, Alexandros Stamatakis2

4/24/25

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

4/24/25

Ezra Bailey, … Oleksiy Kozlov8

4/9/25

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

4/9/25

Alexandros Stamatakis

3/26/25

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

3/26/25

Kenta Renard, Oleksiy Kozlov2

3/19/25

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

3/19/25