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1–30 of 2016
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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Edson Alexandre
,
Alexandros Stamatakis
3
Jul 11
Bootstrap problem
You should re-infer the best ML tree on the reduced alignment that you used as input for
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Bootstrap problem
You should re-infer the best ML tree on the reduced alignment that you used as input for
Jul 11
Alexandros Stamatakis
Jul 9
Looking for an excuse to visit Greece and learn more about Evolutionary and Comparative Genomics?
Join us in Nafplio in November: https://meetings.embo.org/event/24-genomics Alexis -- Alexandros (
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Looking for an excuse to visit Greece and learn more about Evolutionary and Comparative Genomics?
Join us in Nafplio in November: https://meetings.embo.org/event/24-genomics Alexis -- Alexandros (
Jul 9
Luís Crespo
,
Alexandros Stamatakis
2
Jul 9
dumb question: rapid bootstrap support value
Dear Luis, > I feel a bit embarrassed just by asking this, but I can't find a mention > to
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dumb question: rapid bootstrap support value
Dear Luis, > I feel a bit embarrassed just by asking this, but I can't find a mention > to
Jul 9
Kenta Renard
, …
Oleksiy Kozlov
3
Jul 4
Empirical vs ML-optimised frequencies
Dear Kenta, IIRC empirical frequencies are also considered free parameters in ModelTest-NG and RAxML-
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Empirical vs ML-optimised frequencies
Dear Kenta, IIRC empirical frequencies are also considered free parameters in ModelTest-NG and RAxML-
Jul 4
Aram Valafar
,
Alexandros Stamatakis
2
Jun 28
Re: RAxML GPU Cluster Implementation
Dear Aram, > I am a PhD student researching Mycobacterium tuberculosis. RAxML is > extremely
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Re: RAxML GPU Cluster Implementation
Dear Aram, > I am a PhD student researching Mycobacterium tuberculosis. RAxML is > extremely
Jun 28
Stepan Puhov
,
Oleksiy Kozlov
10
Jun 17
Support for site-specific frequency profiles
Hi Oleksiy, Ok, got it. It is quite a relief to read) Of note: the description of the +BU{} option
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Support for site-specific frequency profiles
Hi Oleksiy, Ok, got it. It is quite a relief to read) Of note: the description of the +BU{} option
Jun 17
Lída Veselá
,
Oleksiy Kozlov
3
Jun 11
warning - The model you specified on the command line will be ignored
Dear Oleksiy, thank you very much for fast help and verification, that run was without problems. Best
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warning - The model you specified on the command line will be ignored
Dear Oleksiy, thank you very much for fast help and verification, that run was without problems. Best
Jun 11
Lída Veselá
Jun 10
warning: The model you specified on the command line will be ignored
Dear all, I would like to ask you for advice. I have 401 protein sequences alignment after trimm.
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warning: The model you specified on the command line will be ignored
Dear all, I would like to ask you for advice. I have 401 protein sequences alignment after trimm.
Jun 10
Kenta Renard
, …
Grimm
5
Jun 3
Suspected LBA but high bootstrap value
Hi Kenta, in case of prokaryotic data, split LWRs may have different reasons: uncertainty, lack of
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Suspected LBA but high bootstrap value
Hi Kenta, in case of prokaryotic data, split LWRs may have different reasons: uncertainty, lack of
Jun 3
Jeff Mangot
,
Alexandros Stamatakis
2
May 31
PaPaRa error "vector::_M_range_check" on protein tree/alignment
Which version of Papara are you using? Could you perhaps send me the input files? Alexis On 30.05.24
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PaPaRa error "vector::_M_range_check" on protein tree/alignment
Which version of Papara are you using? Could you perhaps send me the input files? Alexis On 30.05.24
May 31
Alexandros Stamatakis
, …
Lucas Czech
11
May 31
Re: [raxml] EPA-ng "Incompatible partition"
Lucas, I already have them will fwd them to you, Alexis On 29.05.24 18:06, Lucas Czech wrote: > Hi
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Re: [raxml] EPA-ng "Incompatible partition"
Lucas, I already have them will fwd them to you, Alexis On 29.05.24 18:06, Lucas Czech wrote: > Hi
May 31
Arianna Thomas-Cabianca
, …
Oleksiy Kozlov
4
May 31
GTRGAMMAI model in RaxML-ng
Thank you very much Alexandros and Oleksiy El mié, 29 may 2024 a la(s) 9:48 am, Oleksiy Kozlov (
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GTRGAMMAI model in RaxML-ng
Thank you very much Alexandros and Oleksiy El mié, 29 may 2024 a la(s) 9:48 am, Oleksiy Kozlov (
May 31
Jed
,
Oleksiy Kozlov
3
May 24
ERROR in SPR round (LIBPLL-3584) Constraint check failed after reinsert_nodes() in SPR r ound!
Oleksiy, That worked! Thank you. Jed On Tuesday, May 21, 2024 at 8:14:01 AM UTC-4 Oleksiy Kozlov
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ERROR in SPR round (LIBPLL-3584) Constraint check failed after reinsert_nodes() in SPR r ound!
Oleksiy, That worked! Thank you. Jed On Tuesday, May 21, 2024 at 8:14:01 AM UTC-4 Oleksiy Kozlov
May 24
astrid cruaud
, …
Grimm
10
May 22
Morphological dataset: polymorphic characters
Hi all, I don't think that implementing an explicit polymorphism model would make sense because
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Morphological dataset: polymorphic characters
Hi all, I don't think that implementing an explicit polymorphism model would make sense because
May 22
Kenta Renard
, …
Alexandros Stamatakis
5
May 11
Best a posteriori tree rooting options
Dear Kenta, Just to add to this: > Thank you very much for your detailed and helpful response. If
unread,
Best a posteriori tree rooting options
Dear Kenta, Just to add to this: > Thank you very much for your detailed and helpful response. If
May 11
Karthick Babu Sivakumar
, …
Alexandros Stamatakis
4
May 11
How to run raxml on alignment files at genome level
Thank you for the information. On Tue, 7 May, 2024, 9:48 pm Grimm, <grim...@gmail.com> wrote:
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How to run raxml on alignment files at genome level
Thank you for the information. On Tue, 7 May, 2024, 9:48 pm Grimm, <grim...@gmail.com> wrote:
May 11
Kaushik Komandur
,
Anastasis Togkousidis
3
May 6
Obtaining Model Parameters from a Checkpoint Tree
This is super useful. Thank you for the detailed reply! Best, Kaushik On Friday, May 3, 2024 at 9:54:
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Obtaining Model Parameters from a Checkpoint Tree
This is super useful. Thank you for the detailed reply! Best, Kaushik On Friday, May 3, 2024 at 9:54:
May 6
Pailler Vincent
,
Oleksiy Kozlov
10
May 2
Get bootstrap values on consensus tree
yes it's OK, just make sure you specify distinct --seed for each job! On 02.05.24 17:40, Pailler
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Get bootstrap values on consensus tree
yes it's OK, just make sure you specify distinct --seed for each job! On 02.05.24 17:40, Pailler
May 2
Marco Mancuso
,
Oleksiy Kozlov
6
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 Kozlov
4
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 Kozlov
4
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 Stamatakis
2
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 Kozlov
3
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, Wayne
2
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 Kozlov
3
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 Kozlov
8
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
,
Alexis
4
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 Kozlov
4
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 Stamatakis
3
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