raxml

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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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Nanzhen

Oct 14

'--force perf_threads' and CPU core oversubscription detected!

Dear all, I have checked a similar question brought on Oct 19, 2020. But still, I have a few

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'--force perf_threads' and CPU core oversubscription detected!

Dear all, I have checked a similar question brought on Oct 19, 2020. But still, I have a few

Oct 14

Patrik Medstrand, Alexey Kozlov3

Oct 12

Starting trees

Thanks a lot for your response! I will ask the administrators to make v.1.0.3 available Kind regards

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Starting trees

Thanks a lot for your response! I will ask the administrators to make v.1.0.3 available Kind regards

Oct 12

‍최승지[ 직원 / 내과학교실 ], … Pfeiffer, Wayne4

Oct 7

Compilation Issue

Hi, You could use the CIPRES gateway at www.phylo.org If you do not need more than 1000 core hours,

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Compilation Issue

Hi, You could use the CIPRES gateway at www.phylo.org If you do not need more than 1000 core hours,

Oct 7

beli...@gmx.de, Alexandros Stamatakis5

Oct 7

Estimating & saving several RAXML trees with branch lengths

Ok. I see. Thank you. That indeed helps me a lot. Best wishes, Belinda Alexis schrieb am Donnerstag,

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Estimating & saving several RAXML trees with branch lengths

Ok. I see. Thank you. That indeed helps me a lot. Best wishes, Belinda Alexis schrieb am Donnerstag,

Oct 7

Alexandros Stamatakis

Oct 7

12th summer school on computational molecular evolution - July 18-29 2022 Hinxton, UK

Dear Users, Applications for the 12th summer school on computational molecular evolution organized by

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12th summer school on computational molecular evolution - July 18-29 2022 Hinxton, UK

Dear Users, Applications for the 12th summer school on computational molecular evolution organized by

Oct 7

Alexandros Stamatakis

Oct 7

The RAxML Grove: An Empirical Phylogenetic Tree Database

Dear Users of RAxML, As this might be of interest to you I am posting this here as well: The RAxML

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The RAxML Grove: An Empirical Phylogenetic Tree Database

Dear Users of RAxML, As this might be of interest to you I am posting this here as well: The RAxML

Oct 7

Nicolás Peñafiel, Alexey Kozlov5

Sep 30

RAxML-NG 1.0.1 bootstrap: "terminate called recursively"

Hi Nicolas, thanks for sending the files! I can confirm there is a problem, and it looks very similar

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RAxML-NG 1.0.1 bootstrap: "terminate called recursively"

Hi Nicolas, thanks for sending the files! I can confirm there is a problem, and it looks very similar

Sep 30

Nanzhen, Alexey Kozlov2

Sep 28

phylogenetic tree construction commands & time

Hello Nanzhen, your dataset is pretty big, so long running time is expected. Here is what I can

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phylogenetic tree construction commands & time

Hello Nanzhen, your dataset is pretty big, so long running time is expected. Here is what I can

Sep 28

beli...@gmx.de, Grimm2

Sep 27

Problem with Partitions: ERROR trying to assign model

Hi Belinda, the partition file seems indeed to be in order. The 103xx block is not the problem; the

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Problem with Partitions: ERROR trying to assign model

Hi Belinda, the partition file seems indeed to be in order. The 103xx block is not the problem; the

Sep 27

Jeffrey Chiu, Alexandros Stamatakis2

Sep 22

raxml distance loading into R for ordination analysis

I am not sure which distance matrix you mean as it outputs several. Maybe you could paste in an

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raxml distance loading into R for ordination analysis

I am not sure which distance matrix you mean as it outputs several. Maybe you could paste in an

Sep 22

Aderounmu Adedeji, Alexey Kozlov2

Sep 6

SH test

Hi Aderounmu, RAXML-NG can generate per-site log-likelihood scores: raxml-ng --sitelh --msa ali.phy -

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SH test

Hi Aderounmu, RAXML-NG can generate per-site log-likelihood scores: raxml-ng --sitelh --msa ali.phy -

Sep 6

HA, Alexey Kozlov14

Sep 6

ancestral state id

perfect, thanks for the confirmation! On 01.09.21 10:37, HA wrote: > Hi Alexey! > Thanks for

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ancestral state id

perfect, thanks for the confirmation! On 01.09.21 10:37, HA wrote: > Hi Alexey! > Thanks for

Sep 6

ravindra raut, Alexandros Stamatakis2

Sep 5

how get time tree in MYA using RAxML-NG

You need to run a program for divergence time estimation (eg, BEAST) using the tree you obtained from

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how get time tree in MYA using RAxML-NG

You need to run a program for divergence time estimation (eg, BEAST) using the tree you obtained from

Sep 5

Alexandros Stamatakis

Sep 1

NetRAX software for Maximum Likelihood based inference of phylogenetic networks

Dear Users, As you might be interested in this, our new software for maximum likelihood based

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NetRAX software for Maximum Likelihood based inference of phylogenetic networks

Dear Users, As you might be interested in this, our new software for maximum likelihood based

Sep 1

James Munro, Alexandros Stamatakis3

Aug 30

--bootstop-perms & -# autoMRE

Thank you for the insight and advice, Alexis! James On Wednesday, August 25, 2021 at 11:47:46 PM UTC-

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--bootstop-perms & -# autoMRE

Thank you for the insight and advice, Alexis! James On Wednesday, August 25, 2021 at 11:47:46 PM UTC-

Aug 30

Nanzhen, … Alexey Kozlov4

Aug 29

Error - Option -T does not have any effect with the sequential or parallel MPI version.

Hi Grimm and Alexey, Many thanks for the help! Best, Nanzhen 在2021年8月25日星期三 UTC-6 上午6:21:33<alexei

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Error - Option -T does not have any effect with the sequential or parallel MPI version.

Hi Grimm and Alexey, Many thanks for the help! Best, Nanzhen 在2021年8月25日星期三 UTC-6 上午6:21:33<alexei

Aug 29

Justin Bernstein, Alexey Kozlov6

Aug 27

raxml-ng extremely slow on HPC

> Thank you for the advice. I will run it and also check the thread pinning. For the checkpoints,

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raxml-ng extremely slow on HPC

> Thank you for the advice. I will run it and also check the thread pinning. For the checkpoints,

Aug 27

mfonse...@gmail.com, … Lucas Czech6

Aug 26

papara install errors

Hi Mariana, that is a weird MacOS error... are you sure you are using the papara version that you

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papara install errors

Hi Mariana, that is a weird MacOS error... are you sure you are using the papara version that you

Aug 26

Marwa Tawfik

Aug 25

using raxml-ng in R?

Hi everyone, Anyone have experience using raxml-ng in r? I can't find a way to use raxml-ng in

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using raxml-ng in R?

Hi everyone, Anyone have experience using raxml-ng in r? I can't find a way to use raxml-ng in

Aug 25

fhilde, … Alexey Kozlov3

Aug 25

Using RAxML or ExaML with features instead of dna or porteins

thank you, Wayne! On 20.08.21 09:57, Pfeiffer, Wayne wrote: > Hi Felix, > > Both RAxML8 and

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Using RAxML or ExaML with features instead of dna or porteins

thank you, Wayne! On 20.08.21 09:57, Pfeiffer, Wayne wrote: > Hi Felix, > > Both RAxML8 and

Aug 25

Kevin Myers, Alexey Kozlov4

Aug 25

Running RAxML-ng with GTDBTk MSA file

perfect, you are welcome! Alexey On 20.08.21 16:23, Kevin Myers wrote: > Thank you! This response

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Running RAxML-ng with GTDBTk MSA file

perfect, you are welcome! Alexey On 20.08.21 16:23, Kevin Myers wrote: > Thank you! This response

Aug 25

Mike, … Alexey Kozlov11

Aug 25

Trouble running RAxML-MPI on cluster.

Hi Carolina, you should replace "N" with "-" (gap) in your alignment. See error

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Trouble running RAxML-MPI on cluster.

Hi Carolina, you should replace "N" with "-" (gap) in your alignment. See error

Aug 25

Josh D'Aeth, Alexey Kozlov3

Aug 16

raxml-ng ancestral reconstruction inserts amino acid codes into nucleotide alignment

Hi Alexey Great, thanks for clearing that up! Cheers Josh On Monday, August 16, 2021 at 11:34:03 AM

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raxml-ng ancestral reconstruction inserts amino acid codes into nucleotide alignment

Hi Alexey Great, thanks for clearing that up! Cheers Josh On Monday, August 16, 2021 at 11:34:03 AM

Aug 16

Karla Vargas, Alexey Kozlov2

Aug 11

Consel input from RAxML-NG ?

Hi Karla, I think you need per-site log-likelihood scores, which you can generate with the "--

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Consel input from RAxML-NG ?

Hi Karla, I think you need per-site log-likelihood scores, which you can generate with the "--

Aug 11

DC, Alexandros Stamatakis11

Aug 6

partition file error

Hi, Just small update. It is finaly working. It worked at the end when I put whole directorium path

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partition file error

Hi, Just small update. It is finaly working. It worked at the end when I put whole directorium path

Aug 6

shenxing...@gmail.com, Alexey Kozlov2

Aug 2

save intermediate tree / locally optimal tree

Hi Xing. raxml-ng will store current-best tree into PREFIX.raxml.lastTree.TMP file, however this file

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save intermediate tree / locally optimal tree

Hi Xing. raxml-ng will store current-best tree into PREFIX.raxml.lastTree.TMP file, however this file

Aug 2

Anitha Bavikatte, Alexey Kozlov3

Jul 29

Re: phylogenetic tree construction time

Thanks for reply. Raxml already created model that's why I started using bootstrap. This option

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Re: phylogenetic tree construction time

Thanks for reply. Raxml already created model that's why I started using bootstrap. This option

Jul 29

SoniaN, … Grimm3

Jul 28

indel coding

Hi Sonia, adding to Alexi, pending the complexity of your indels, you can use the binary option to

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indel coding

Hi Sonia, adding to Alexi, pending the complexity of your indels, you can use the binary option to

Jul 28

Martin Wu, Pierre Barbera2

Jul 23

running slow EPA algorithm

Dear Martin, the "fast" algorithm will still determine the best insertion location along

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running slow EPA algorithm

Dear Martin, the "fast" algorithm will still determine the best insertion location along

Jul 23

shaohong feng, … Alexey Kozlov3

Jul 19

Estimate branch length with a fixed tree

please use raxml-ng --evaluate command: https://github.com/amkozlov/raxml-ng/wiki/Tutorial#tree-

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Estimate branch length with a fixed tree

please use raxml-ng --evaluate command: https://github.com/amkozlov/raxml-ng/wiki/Tutorial#tree-

Jul 19