raxml

1–30 of 1799

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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Nicolás Peñafiel

Sep 20

RAxML-NG 1.0.1 bootstrap: "terminate called recursively"

Dear community: I have been having an issue when running bootstrap for my tree. After starting, at

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RAxML-NG 1.0.1 bootstrap: "terminate called recursively"

Dear community: I have been having an issue when running bootstrap for my tree. After starting, at

Sep 20

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

KUKU, Alexandros Stamatakis2

Jul 19

Bootstrap trees

Dear Kanishka, Sorry for the late reply, your message ended up in my SPAM folder. If you are using

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Bootstrap trees

Dear Kanishka, Sorry for the late reply, your message ended up in my SPAM folder. If you are using

Jul 19

wes, … Grimm3

Jul 9

Bootstrapping

I'd like to add that one has little problem publishing bootstrap values using RAxML's

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Bootstrapping

I'd like to add that one has little problem publishing bootstrap values using RAxML's

Jul 9

Marta Álvarez, Alexey Kozlov4

Jul 6

Raxml-ng error

Hi Marta, thank you for reporting back! Alexey On 06.07.21 13:24, Marta Álvarez wrote: > Hi, >

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Raxml-ng error

Hi Marta, thank you for reporting back! Alexey On 06.07.21 13:24, Marta Álvarez wrote: > Hi, >

Jul 6

Daniel Lundin, … Grimm11

Jul 5

Taxonomy constrained reference 16S tree

Re: "I clustered the sequences at 85% identity to get a set of slightly more than 1000 sequences

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Taxonomy constrained reference 16S tree

Re: "I clustered the sequences at 85% identity to get a set of slightly more than 1000 sequences

Jul 5

gabriele...@gmail.com, Alexandros Stamatakis3

Jul 1

Concatenated-sequences tree VS gene trees

Hi Alexis, Thank you for your reply, and for clarifying some of my comments/questions. I asked the

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Concatenated-sequences tree VS gene trees

Hi Alexis, Thank you for your reply, and for clarifying some of my comments/questions. I asked the

Jul 1

Mergi Daba, … gabriele...@gmail.com12

Jun 30

gene tree in raxml!

Dear Gabriele Thank you for your reply. I will go by your suggestion and try out. Best, On Wed, Jun

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gene tree in raxml!

Dear Gabriele Thank you for your reply. I will go by your suggestion and try out. Best, On Wed, Jun

Jun 30

Shilpi Nagpal, Alexandros Stamatakis2

Jun 24

Regarding using RAxML

It might indeed be better if you download it and run it locally as the datasets could exceed run time

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Regarding using RAxML

It might indeed be better if you download it and run it locally as the datasets could exceed run time

Jun 24

abs, … Alexandros Stamatakis6

Jun 24

ancestral state construction made longer sequences for parents

Hello! I don't know what exact problem you have, but I made it this way. I had one initial tree ,

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ancestral state construction made longer sequences for parents

Hello! I don't know what exact problem you have, but I made it this way. I had one initial tree ,

Jun 24

Steven Tavis, Alexey Kozlov3

Jun 11

conflicting requirements for --tree when using comprehensive constraint tree

Hi Alexi, Thank you. Steven On Thursday, June 10, 2021 at 7:44:11 PM UTC-4 alexei...@gmail.com wrote:

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conflicting requirements for --tree when using comprehensive constraint tree

Hi Alexi, Thank you. Steven On Thursday, June 10, 2021 at 7:44:11 PM UTC-4 alexei...@gmail.com wrote:

Jun 11