raxml

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1–30 of 2001

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

Apr 20

Support for site-specific frequency profiles

Dear RAxML team, Do you have any plans for adding support for user-defined site-specific AA-frequency

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Support for site-specific frequency profiles

Dear RAxML team, Do you have any plans for adding support for user-defined site-specific AA-frequency

Apr 20

Pailler Vincent, Oleksiy Kozlov8

Apr 19

Get bootstrap values on consensus tree

Thanks I run the MRE bootstrap with the msa file then. I will use --support to add the values on my

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Get bootstrap values on consensus tree

Thanks I run the MRE bootstrap with the msa file then. I will use --support to add the values on my

Apr 19

Marco Mancuso, Oleksiy Kozlov6

Apr 17

installation issue involving the make command and syntax errors.

Hi Marco, > Thank you so much! It works now :). > I managed to make this version work in the

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installation issue involving the make command and syntax errors.

Hi Marco, > Thank you so much! It works now :). > I managed to make this version work in the

Apr 17

Pascal Title, Oleksiy Kozlov4

Apr 10

generating bootstraps with fixed topology, running into error

Perfect, if possible please send the input files BOOT.raxml.bootstrapMSA.1.phy BOOT.raxml.

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generating bootstraps with fixed topology, running into error

Perfect, if possible please send the input files BOOT.raxml.bootstrapMSA.1.phy BOOT.raxml.

Apr 10

Michael Tassia, Oleksiy Kozlov4

Apr 10

Unphased diploid genotypes rates vector

There seems to be a discrepancy between supplementary note and the actual implementation wrt rate

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Unphased diploid genotypes rates vector

There seems to be a discrepancy between supplementary note and the actual implementation wrt rate

Apr 10

Geert Roks, Alexandros Stamatakis2

Apr 8

Single precision implementation of Phylogenetic Likelihood Kernel (newviewGTRGAMMA) in standard-RAxML

Dear Geert, We basically completely abandoned any further attempts with single precision as it was

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Single precision implementation of Phylogenetic Likelihood Kernel (newviewGTRGAMMA) in standard-RAxML

Dear Geert, We basically completely abandoned any further attempts with single precision as it was

Apr 8

Kenta Renard, Oleksiy Kozlov3

Mar 29

Issues with --bsconverge command

Dear Oleksiy, I managed to solve it, I just had to use a new terminal. Best, Kenta On Tuesday 26

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Issues with --bsconverge command

Dear Oleksiy, I managed to solve it, I just had to use a new terminal. Best, Kenta On Tuesday 26

Mar 29

chiara Sgaramella, Pfeiffer, Wayne2

Mar 22

Core phylogenetic tree/CIPRES

Please use RAxML-NG on ACCESS to run RAxML-NG via CIPRES. On Mar 21, 2024, at 6:53 AM, chiara

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Core phylogenetic tree/CIPRES

Please use RAxML-NG on ACCESS to run RAxML-NG via CIPRES. On Mar 21, 2024, at 6:53 AM, chiara

Mar 22

Andrew ODonnell, Oleksiy Kozlov3

Mar 9

raxml-ng not starting with defined starting tree number?

Wow... that was silly of me. Thanks for your quick reply! On Fri, Mar 8, 2024 at 8:49 PM Oleksiy

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raxml-ng not starting with defined starting tree number?

Wow... that was silly of me. Thanks for your quick reply! On Fri, Mar 8, 2024 at 8:49 PM Oleksiy

Mar 9

taua...@gmail.com, … Oleksiy Kozlov8

Mar 5

Restarting RAxML from checkpoint

Dear Andrew, thanks for your feedback! Best, Oleksiy On 05.03.24 08:34, Andrew ODonnell wrote: >

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Restarting RAxML from checkpoint

Dear Andrew, thanks for your feedback! Best, Oleksiy On 05.03.24 08:34, Andrew ODonnell wrote: >

Mar 5

Sithions Brand, Alexis4

Mar 4

bias correction for help

Maybe the script is not removing sites containing a single character but also some gaps and

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bias correction for help

Maybe the script is not removing sites containing a single character but also some gaps and

Mar 4

Sithions Brand

Feb 27

Ascertainment bias correction-raxml

Hi everyone, For the SNPs generated by GBS-SNP-CROP software to build a phylogenetic tree, whether to

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Ascertainment bias correction-raxml

Hi everyone, For the SNPs generated by GBS-SNP-CROP software to build a phylogenetic tree, whether to

Feb 27

Ugo Bastolla, Oleksiy Kozlov4

Feb 19

Branch length scaling

> Thank you very much for the fast answer Oleksiy! > My problems is how does raxml rescale the

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Branch length scaling

> Thank you very much for the fast answer Oleksiy! > My problems is how does raxml rescale the

Feb 19

Maiara Moro, Alexandros Stamatakis3

Feb 9

Normalization of Genetic Distances (raxml -f x)

Thank you very much, Alexis. It helped a lot! On Thu, 8 Feb 2024 at 04:41, Alexandros Stamatakis <

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Normalization of Genetic Distances (raxml -f x)

Thank you very much, Alexis. It helped a lot! On Thu, 8 Feb 2024 at 04:41, Alexandros Stamatakis <

Feb 9

Abdulrahman Murad, Oleksiy Kozlov3

Feb 8

Substitution Model Selection in RAxML-NG

Thanks a lot ! Appreciate the help On Monday 5 February 2024 at 17:35:40 UTC+3 Oleksiy Kozlov wrote:

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Substitution Model Selection in RAxML-NG

Thanks a lot ! Appreciate the help On Monday 5 February 2024 at 17:35:40 UTC+3 Oleksiy Kozlov wrote:

Feb 8

Marco Mancuso, Alexandros Stamatakis2

Feb 6

-f a -x bootstrapping prompted error

I think the problem might be an extra space or invalid character you might have added somewhere, eg,

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-f a -x bootstrapping prompted error

I think the problem might be an extra space or invalid character you might have added somewhere, eg,

Feb 6

Steve Haddock, Oleksiy Kozlov2

Feb 1

Is there a --quiet or --verbose=0 option for raxml-ng

Hi Steve, you can use "--log ERROR" to suppress all output, however this will also affect

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Is there a --quiet or --verbose=0 option for raxml-ng

Hi Steve, you can use "--log ERROR" to suppress all output, however this will also affect

Feb 1

Sithions Brand, Grimm5

Jan 28

SNPs-Ambiguous base

Dear Dr.Grimm, Thank you for your advice！ Cheers, Brand 在2024年1月24日星期三 UTC+8 16:47:00<Grimm> 写道

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SNPs-Ambiguous base

Dear Dr.Grimm, Thank you for your advice！ Cheers, Brand 在2024年1月24日星期三 UTC+8 16:47:00<Grimm> 写道

Jan 28

Aline Silva, … Alexandros Stamatakis7

Jan 27

Not recognized as an internal or external command, operable program, or batch file

Yes please try raxml-ng first, but as I said the problem is that your computer does not find the

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Not recognized as an internal or external command, operable program, or batch file

Yes please try raxml-ng first, but as I said the problem is that your computer does not find the

Jan 27

Brandon Stark, Alexandros Stamatakis2

Jan 27

what is the different between G4 and G4m, thanks.

See: https://github.com/amkozlov/raxml-ng/wiki/Input-data#evolutionary-model I think they are

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what is the different between G4 and G4m, thanks.

See: https://github.com/amkozlov/raxml-ng/wiki/Input-data#evolutionary-model I think they are

Jan 27

Wyclif Odago, … Alexandros Stamatakis7

Jan 27

Gene-tree generation

Hi Chase, Thanks for reporting, it would be good if you could share the de-identified data with

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Gene-tree generation

Hi Chase, Thanks for reporting, it would be good if you could share the de-identified data with

Jan 27

Miao Sun, Oleksiy Kozlov2

Jan 24

Assertion `num_models == m.size()' failed.

Dear Miao, yes please always attach full log file, and ideally input files. Thanks, Oleksiy On 24.01.

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Assertion `num_models == m.size()' failed.

Dear Miao, yes please always attach full log file, and ideally input files. Thanks, Oleksiy On 24.01.

Jan 24

gyk...@gmail.com, Oleksiy Kozlov2

Jan 18

dependency versions

Dear Gyozo, > I am trying to install RAxML-NG v1.2.1 and did succeed using pre-compiled binaries.

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dependency versions

Dear Gyozo, > I am trying to install RAxML-NG v1.2.1 and did succeed using pre-compiled binaries.

Jan 18

Alexandros Stamatakis

Jan 16

Crete May 2024 - Machine Learning for Evolutionary Genomics Data

Dear Users of our Software, Sorry for bothering you with some event advertisement again via this list

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Crete May 2024 - Machine Learning for Evolutionary Genomics Data

Dear Users of our Software, Sorry for bothering you with some event advertisement again via this list

Jan 16

rutge...@naturalis.nl, Grimm4

Jan 8

Constraint tree construction strategy

Hi Rutger, there may be an intermediate filtering step needed, particularly since your are interested

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Constraint tree construction strategy

Hi Rutger, there may be an intermediate filtering step needed, particularly since your are interested

Jan 8

Daniel Lundin, Oleksiy Kozlov6

12/22/23

Problems with Sativa Conda package

Den fre 22 dec. 2023 kl 18:43 skrev Oleksiy Kozlov <alexei...@gmail.com>: > > Hi

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Problems with Sativa Conda package

Den fre 22 dec. 2023 kl 18:43 skrev Oleksiy Kozlov <alexei...@gmail.com>: > > Hi

12/22/23

Daryl Lam, … Tobias Senoner9

12/20/23

Issue using RaxML-ng to make an ExaBayes consensus tree

Hi Oleksiy, Thank you for your response and for the solution. The tree I mentioned was just a basic

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Issue using RaxML-ng to make an ExaBayes consensus tree

Hi Oleksiy, Thank you for your response and for the solution. The tree I mentioned was just a basic

12/20/23

Gustavo Avelar Molina, … Alexandros Stamatakis3

12/20/23

How to improve the ratio between alignment sites and number of free parameters?

Dear Gustavo, I guess the problem are the branch lengths that are free parameters of the model. So,

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How to improve the ratio between alignment sites and number of free parameters?

Dear Gustavo, I guess the problem are the branch lengths that are free parameters of the model. So,

12/20/23

Grimm, Kevin Myers7

12/8/23

Re: RAxML-NG running extremely slowly

Thanks. The alignment looks good to my eye, but I will try some of the other tips you suggest! I also

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Re: RAxML-NG running extremely slowly

Thanks. The alignment looks good to my eye, but I will try some of the other tips you suggest! I also

12/8/23

Kevin Myers, Oleksiy Kozlov3

12/7/23

RAxML running extremely slowly

Thanks. I will download the new version and try that. On Thursday, December 7, 2023 at 9:24:17 AM UTC

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RAxML running extremely slowly

Thanks. I will download the new version and try that. On Thursday, December 7, 2023 at 9:24:17 AM UTC

12/7/23