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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.
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Scarivanny
, …
Oleksiy Kozlov
4
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/
unread,
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 Kozlov
3
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, Johannes
4
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
unread,
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 Stamatakis
2
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
unread,
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 Kozlov
8
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 Minh
8
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 Kozlov
2
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 Stamatakis
3
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
unread,
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 Kozlov
3
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 Kozlov
2
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
, …
Grimm
5
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
unread,
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 Togkousidis
3
Feb 7
RAxML-NG 2 (dev version) questions
Dear Kenta, If you intend to publish any results inferred from the current adaptive heuristic in
unread,
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
, …
Grimm
4
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
unread,
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 Kozlov
3
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
unread,
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 Kozlov
3
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 Kozlov
4
Jan 6
analysis time
Dear Oleksiy, Thanks for the response and the new updates to the program. Please find attached log
unread,
analysis time
Dear Oleksiy, Thanks for the response and the new updates to the program. Please find attached log
Jan 6
Grimm
, …
Oleksiy Kozlov
9
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://
unread,
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
,
Grimm
2
11/27/24
Re: [raxml] Bad base () error
Hi Patricia, one problem (most probably) is that the intermediate "paupdata.txt" has the
unread,
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 Kozlov
2
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 Kozlov
4
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 Kozlov
3
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
unread,
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, Wayne
8
11/4/24
Estimated Bootstrap Guesser
Hi Oleksiy, Thanks for the suggestion regarding my testing for AA data. I did indeed input a newick
unread,
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 Kozlov
4
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,
unread,
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 Stamatakis
2
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
unread,
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
unread,
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