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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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Vân Nguyễn

Mar 12

RNA models and bootstrap values of trees inferred with RNA models

Hi everyone, I'm working on a project to infer phylogenetic trees while incorporating RNA

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RNA models and bootstrap values of trees inferred with RNA models

Hi everyone, I'm working on a project to infer phylogenetic trees while incorporating RNA

Mar 12

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

Yasuto ISHII, Oleksiy Kozlov3

Feb 4

Reference on phylogenetic analysis using genotype likelihood data

Hi Oleksiy, Thanks a lot! Best, Yasuto 2025年2月4日火曜日 22:47:38 UTC+9 Oleksiy Kozlov: Hi Yasuto, this

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Reference on phylogenetic analysis using genotype likelihood data

Hi Oleksiy, Thanks a lot! Best, Yasuto 2025年2月4日火曜日 22:47:38 UTC+9 Oleksiy Kozlov: Hi Yasuto, this

Feb 4

Émilie Tremblay, … Oleksiy Kozlov3

Jan 17

Model specified gets ignored

Hi Émilie, > raxml-ng --msa /home/tremblayemi/nfcore/rawData/results/fungi-and-controls_v2/dada2/

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Model specified gets ignored

Hi Émilie, > raxml-ng --msa /home/tremblayemi/nfcore/rawData/results/fungi-and-controls_v2/dada2/

Jan 17

chris blair, Oleksiy Kozlov4

Jan 6

analysis time

Dear Oleksiy, Thanks for the response and the new updates to the program. Please find attached log

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analysis time

Dear Oleksiy, Thanks for the response and the new updates to the program. Please find attached log

Jan 6

Grimm, … Oleksiy Kozlov9

12/12/24

Re: RAxML-NG running extremely slowly

for AA data, you should use one of the protein models such as LG instead of GTR, please see: https://

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Re: RAxML-NG running extremely slowly

for AA data, you should use one of the protein models such as LG instead of GTR, please see: https://

12/12/24

Patricia Torres-Pineda, … Grimm3

11/27/24

Bad base () error

Hi Patricia, one problem (most probably) is that the intermediate "paupdata.txt" has the

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Bad base () error

Hi Patricia, one problem (most probably) is that the intermediate "paupdata.txt" has the

11/27/24

Kenta Renard, Oleksiy Kozlov2

11/25/24

Coarse-grained parallelisation efficiency in RAxML-NG

Dear Kenta, depending on your dataset and hardware, the could be efficiency loss or efficiency gain.

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Coarse-grained parallelisation efficiency in RAxML-NG

Dear Kenta, depending on your dataset and hardware, the could be efficiency loss or efficiency gain.

11/25/24

Sithions Brand, Oleksiy Kozlov4

11/17/24

Partitionfinder models for raxml

Dear Prof Kozlov, Thank you for help! Best wishes Sithions 在2024年11月13日星期三 UTC+8 19:46:46<Oleksiy

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Partitionfinder models for raxml

Dear Prof Kozlov, Thank you for help! Best wishes Sithions 在2024年11月13日星期三 UTC+8 19:46:46<Oleksiy

11/17/24

Kenta Renard, Oleksiy Kozlov3

11/16/24

void load_start_trees error

Dear Oleksiy, Yes. With the --redo flag the .mlTrees.TMP file is overwritten and any inferred trees

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void load_start_trees error

Dear Oleksiy, Yes. With the --redo flag the .mlTrees.TMP file is overwritten and any inferred trees

11/16/24

Alexandros Stamatakis, … Pfeiffer, Wayne8

11/4/24

Estimated Bootstrap Guesser

Hi Oleksiy, Thanks for the suggestion regarding my testing for AA data. I did indeed input a newick

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Estimated Bootstrap Guesser

Hi Oleksiy, Thanks for the suggestion regarding my testing for AA data. I did indeed input a newick

11/4/24

benjami...@gmail.com, Oleksiy Kozlov4

11/4/24

Numeric issue in ancestral reconstruction ?

Great, many thanks for testing! On 04.11.24 15:22, benjami...@gmail.com wrote: > Dear Oleksiy,

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Numeric issue in ancestral reconstruction ?

Great, many thanks for testing! On 04.11.24 15:22, benjami...@gmail.com wrote: > Dear Oleksiy,

11/4/24

dv, Alexandros Stamatakis2

10/28/24

run ML search indepedently after rapid bootstrapping

Please not that standard RAxML is not supported any more, you might consider switching to RAxML-NG

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run ML search indepedently after rapid bootstrapping

Please not that standard RAxML is not supported any more, you might consider switching to RAxML-NG

10/28/24

Alexandros Stamatakis

10/21/24

Applications for 2025 computational molecular evolution summer school close in 10 days

Dear Users of our software tools, Applications are still open for the 2025 school on computational

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Applications for 2025 computational molecular evolution summer school close in 10 days

Dear Users of our software tools, Applications are still open for the 2025 school on computational

10/21/24

Alexandros Stamatakis

10/8/24

Applications for 2025 computational molecular evolution summer school close in 3 weeks

Dear Users of our software tools, Applications are still open for the 2025 school on computational

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Applications for 2025 computational molecular evolution summer school close in 3 weeks

Dear Users of our software tools, Applications are still open for the 2025 school on computational

10/8/24

Ana Otero, Alexandros Stamatakis3

10/8/24

Error when trying to constrain through binary backbone

OMG, This is terrible, I'm so sorry Alexandros. I just realized this was all a misunderstanding.

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Error when trying to constrain through binary backbone

OMG, This is terrible, I'm so sorry Alexandros. I just realized this was all a misunderstanding.

10/8/24

Brintha V P cs18d017, … Grimm6

9/30/24

raxml - bootrapping taking too long

Hi, You are right Grimm. After removing the duplicates and taking only the conserved regions in all

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raxml - bootrapping taking too long

Hi, You are right Grimm. After removing the duplicates and taking only the conserved regions in all

9/30/24

*, Grimm2

9/23/24

allele_freq

The problem may be that any non-molecular standard character, which binned characters are using the

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allele_freq

The problem may be that any non-molecular standard character, which binned characters are using the

9/23/24

Ayush Mishra, Alexandros Stamatakis2

9/23/24

RogueNaRok Webserver not Working

We decided to discontinue the RogueNaRok web-service as we don't have capacity to maintain it any

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RogueNaRok Webserver not Working

We decided to discontinue the RogueNaRok web-service as we don't have capacity to maintain it any

9/23/24

Alexandros Stamatakis

9/17/24

Registrations for 2025 computational molecular evolution summer school are open

Dear Users of our software tools, Registrations are open for the 2025 school on computational

unread,

Registrations for 2025 computational molecular evolution summer school are open

Dear Users of our software tools, Registrations are open for the 2025 school on computational

9/17/24

Brandon Stark, Oleksiy Kozlov2

9/13/24

what is the option in raxml-ng for `-U` in raxml?

This particular memory saving option is not implemented in raxml-ng. However, raxml-ng uses site

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what is the option in raxml-ng for `-U` in raxml?

This particular memory saving option is not implemented in raxml-ng. However, raxml-ng uses site

9/13/24

Alexandros Stamatakis, … Oleksiy Kozlov3

8/23/24

Re: [raxml] "ERROR: Bootstrap tree #1 has wrong number of tips"

Dear Kenta, please post your input files (trees) and full raxml-ng logs file, then you will save us a

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Re: [raxml] "ERROR: Bootstrap tree #1 has wrong number of tips"

Dear Kenta, please post your input files (trees) and full raxml-ng logs file, then you will save us a

8/23/24

Brandon Stark, … Alexandros Stamatakis4

8/18/24

which parameters should I use with the "lot of missing data"?

thanks @Guido and Alexis, this is helpful to me. 在2024年8月12日星期一 UTC+8 20:44:24<Alexandros

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which parameters should I use with the "lot of missing data"?

thanks @Guido and Alexis, this is helpful to me. 在2024年8月12日星期一 UTC+8 20:44:24<Alexandros

8/18/24

Andrea Gasparin, … Lucas Czech4

8/12/24

No way to export from python newick readable by raxml

Another addition: The error seems to happen in a named branch. It could be that you are running into

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No way to export from python newick readable by raxml

Another addition: The error seems to happen in a named branch. It could be that you are running into

8/12/24