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raxml

1–30 of 2058

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.

0 selected

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

unread,

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=

unread,

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

unread,

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

unread,

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

unread,

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

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

Alexandros Stamatakis, Grimm2

11/27/24

Re: [raxml] Bad base () error

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

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Re: [raxml] 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.

unread,

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

unread,

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