command line to estimate only the best-scoring tree
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Juan C. Opazo
Dec 8, 2015, 2:17:22 PM12/8/15
to raxml
Hi guys, I am wondering if you can help me setting up the command line to only obtain the best-scoring ML tree (no bootstrap). I tried:
raxmlHPC-MPI -f d -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -# 20
but I am getting a collection of 20 trees, but not the RAxML.bestTree file.
any help is welcome
Juan
raxmlHPC-MPI -f d -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -# 20
but I am getting a collection of 20 trees, but not the RAxML.bestTree file.
any help is welcome
Juan
Alexandros Stamatakis
Dec 8, 2015, 4:29:29 PM12/8/15
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hi juan,
that's weird, which version of RAxML are you using?
alexis
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Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson
www.exelixis-lab.org
that's weird, which version of RAxML are you using?
alexis
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Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson
www.exelixis-lab.org
Juan C. Opazo
Dec 8, 2015, 4:47:42 PM12/8/15
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Hi Alexis, thank you for your rapid response, I am using RAxML version 8.2.0. I am wondering if is possible to only obtain the best tree, no bootstrap. The reason is that most of the times before to proceed to the bootstrap analysis on the final data set, we explore our data using best trees (because obtaining them is very fast). So in our lab we make tons of best trees before to close our data set and perform support routines (e.g. bootstrap and Bayesian analyses).
Now I tried the following command line which also perform bootstrap, but my trick is to set the -# setting to 2, raxmlHPC-MPI -f a -p 12345 -s Alignment.fasta -x 12345 -# 2 -m PROTGAMMAJTT -n outfile
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Juan C. Opazo
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
fax: 56-63-2221344
jopazo (at) gmail (dot) com
OpazoLab
ResearchGate
Doctorado en Ciencias mención Ecología y Evolución
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
fax: 56-63-2221344
jopazo (at) gmail (dot) com
OpazoLab
ResearchGate
Doctorado en Ciencias mención Ecología y Evolución
Alexandros Stamatakis
Dec 8, 2015, 4:59:28 PM12/8/15
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Hi Juan,
Could it be that your batch queueing system is recognizing -# 20 as
comment, maybe you should try -N 20 which is equivalent.
Also please upgrade to the latest version 8.2.4
Finally, I looked at the code and it should produce a best-scoring tree
file, the end of the output should look something like this below.
Alexis
Starting final GAMMA-based thorough Optimization on tree 11 likelihood
-116.492312 ....
Final GAMMA-based Score of best tree -116.492312
Program execution info written to
/home/stamatak/Desktop/GIT/raxml-hpc/standard-RAxML/RAxML_info.PP6
Best-scoring ML tree written to:
/home/stamatak/Desktop/GIT/raxml-hpc/standard-RAxML/RAxML_bestTree.PP6
Overall execution time: 1.614655 secs or 0.000449 hours or 0.000019 days
On 08.12.2015 22:47, Juan C. Opazo wrote:
> Hi Alexis, thank you for your rapid response, I am using RAxML version
> 8.2.0. I am wondering if is possible to only obtain the best tree, no
> bootstrap. The reason is that most of the times before to proceed to the
> bootstrap analysis on the final data set, we explore our data using best
> trees (because obtaining them is very fast). So in our lab we make tons
> of best trees before to close our data set and perform support routines
> (e.g. bootstrap and Bayesian analyses).
>
> Now I tried the following command line which also perform bootstrap, but
> my trick is to set the -# setting to 2,
>
> raxmlHPC-MPI -f a -p 12345 -s Alignment.fasta -x 12345 -# 2 -m
> PROTGAMMAJTT -n outfile
>
> any help is welcome
>
> juan
>
>
>
>
> On Tue, Dec 8, 2015 at 6:29 PM, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y Evolución <http://www.ecolevol.cl>
Could it be that your batch queueing system is recognizing -# 20 as
comment, maybe you should try -N 20 which is equivalent.
Also please upgrade to the latest version 8.2.4
Finally, I looked at the code and it should produce a best-scoring tree
file, the end of the output should look something like this below.
Alexis
Starting final GAMMA-based thorough Optimization on tree 11 likelihood
-116.492312 ....
Final GAMMA-based Score of best tree -116.492312
Program execution info written to
/home/stamatak/Desktop/GIT/raxml-hpc/standard-RAxML/RAxML_info.PP6
Best-scoring ML tree written to:
/home/stamatak/Desktop/GIT/raxml-hpc/standard-RAxML/RAxML_bestTree.PP6
Overall execution time: 1.614655 secs or 0.000449 hours or 0.000019 days
On 08.12.2015 22:47, Juan C. Opazo wrote:
> Hi Alexis, thank you for your rapid response, I am using RAxML version
> 8.2.0. I am wondering if is possible to only obtain the best tree, no
> bootstrap. The reason is that most of the times before to proceed to the
> bootstrap analysis on the final data set, we explore our data using best
> trees (because obtaining them is very fast). So in our lab we make tons
> of best trees before to close our data set and perform support routines
> (e.g. bootstrap and Bayesian analyses).
>
> Now I tried the following command line which also perform bootstrap, but
> my trick is to set the -# setting to 2,
>
> raxmlHPC-MPI -f a -p 12345 -s Alignment.fasta -x 12345 -# 2 -m
> PROTGAMMAJTT -n outfile
>
> any help is welcome
>
> juan
>
>
>
>
> On Tue, Dec 8, 2015 at 6:29 PM, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> hi juan,
>
> that's weird, which version of RAxML are you using?
>
> alexis
>
> On 08.12.2015 20:17, Juan C. Opazo wrote:
>
> Hi guys, I am wondering if you can help me setting up the
> command line
> to only obtain the best-scoring ML tree (no bootstrap). I tried:
>
> raxmlHPC-MPI -f d -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n
> outfile
> -# 20
>
> but I am getting a collection of 20 trees, but not the
> RAxML.bestTree file.
>
> any help is welcome
>
> Juan
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from
> it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
>
> hi juan,
>
> that's weird, which version of RAxML are you using?
>
> alexis
>
> On 08.12.2015 20:17, Juan C. Opazo wrote:
>
> Hi guys, I am wondering if you can help me setting up the
> command line
> to only obtain the best-scoring ML tree (no bootstrap). I tried:
>
> raxmlHPC-MPI -f d -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n
> outfile
> -# 20
>
> but I am getting a collection of 20 trees, but not the
> RAxML.bestTree file.
>
> any help is welcome
>
> Juan
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from
> it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>
>
> --
> You received this message because you are subscribed to a topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/xh8DcOMULHw/unsubscribe.
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> raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>.
> --
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> raxml+un...@googlegroups.com
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> fax: 56-63-2221344
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> fax: 56-63-2221344
> jopazo (at) gmail (dot) com
>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y Evolución <http://www.ecolevol.cl>
Juan C. Opazo
Dec 8, 2015, 5:02:56 PM12/8/15
to raxml
Thank you Alexis, I´ll check this out and I´ll upgrade to the recommended version.
bestTo unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
--
Juan C. Opazo
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
fax: 56-63-2221344
jopazo (at) gmail (dot) com
OpazoLab
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
fax: 56-63-2221344
jopazo (at) gmail (dot) com
OpazoLab
Juan C. Opazo
Dec 8, 2015, 6:44:58 PM12/8/15
to raxml
Hi Alexis, no luck....I changed -# by -N as you suggested but nothing.......here is the output
do you have any idea?cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$ raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -N 10
This is RAxML MPI Process Number: 0
RAxML can't, parse the alignment file as phylip file
it will now try to parse it as FASTA file
This is RAxML version 8.2.0 released by Alexandros Stamatakis on July 9 2015.
With greatly appreciated code contributions by:
Andre Aberer (HITS)
Simon Berger (HITS)
Alexey Kozlov (HITS)
Kassian Kobert (HITS)
David Dao (KIT and HITS)
Nick Pattengale (Sandia)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (NRIFS)
Alignment has 363 distinct alignment patterns
Proportion of gaps and completely undetermined characters in this alignment: 1.62%
RAxML rapid hill-climbing mode
Using 1 distinct models/data partitions with joint branch length optimization
Executing 10 inferences on the original alignment using 10 distinct randomized MP trees
All free model parameters will be estimated by RAxML
GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Partition: 0
Alignment Patterns: 363
Name: No Name Provided
DataType: AA
Substitution Matrix: JTT
Using fixed base frequencies
RAxML was called as follows:
raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -N 10
Partition: 0 with name: No Name Provided
Base frequencies: 0.077 0.052 0.043 0.052 0.020 0.041 0.062 0.073 0.023 0.054 0.092 0.059 0.024 0.040 0.051 0.069 0.059 0.014 0.032 0.066
Inference[0]: Time 23.651726 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[1]: Time 23.689768 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[2]: Time 23.367036 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[3]: Time 23.416103 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[4]: Time 23.372482 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[5]: Time 23.381697 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[6]: Time 23.303497 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[7]: Time 23.453993 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[8]: Time 23.775530 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[9]: Time 23.782873 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Conducting final model optimizations on all 10 trees under GAMMA-based models ....
Inference[0] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.0
Inference[1] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.1
Inference[2] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.2
Inference[3] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.3
Inference[4] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.4
Inference[5] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.5
Inference[6] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.6
Inference[7] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.7
Inference[8] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.8
Inference[9] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.9
cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$
Alexey Kozlov
Dec 8, 2015, 7:19:26 PM12/8/15
to ra...@googlegroups.com
Dear Juan,
could you try it with more than 1 MPI process? Alternatively, just use sequential version of RAxML if you don't need
parallelization. This should fix the problem.
@Alexis: bestProcess is only initialized if processes > 1, looks like a bug.
Alexey
> <mailto:raxml+un...@googlegroups.com <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com <mailto:raxml%252Buns...@googlegroups.com>>>.
> fax: 56-63-2221344 <tel:56-63-2221344>
> fax: 56-63-2221344 <tel:56-63-2221344>
could you try it with more than 1 MPI process? Alternatively, just use sequential version of RAxML if you don't need
parallelization. This should fix the problem.
@Alexis: bestProcess is only initialized if processes > 1, looks like a bug.
Alexey
> <mailto:alexandros...@gmail.com <mailto:alexandros...@gmail.com>>> wrote:
>
> hi juan,
>
> that's weird, which version of RAxML are you using?
>
> alexis
>
> On 08.12.2015 20:17, Juan C. Opazo wrote:
>
> Hi guys, I am wondering if you can help me setting up the
> command line
> to only obtain the best-scoring ML tree (no bootstrap). I tried:
>
> raxmlHPC-MPI -f d -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n
> outfile
> -# 20
>
> but I am getting a collection of 20 trees, but not the
> RAxML.bestTree file.
>
> any help is welcome
>
> Juan
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from
> it, send
> an email to raxml+un...@googlegroups.com <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com <mailto:raxml%252Buns...@googlegroups.com>>
>
> hi juan,
>
> that's weird, which version of RAxML are you using?
>
> alexis
>
> On 08.12.2015 20:17, Juan C. Opazo wrote:
>
> Hi guys, I am wondering if you can help me setting up the
> command line
> to only obtain the best-scoring ML tree (no bootstrap). I tried:
>
> raxmlHPC-MPI -f d -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n
> outfile
> -# 20
>
> but I am getting a collection of 20 trees, but not the
> RAxML.bestTree file.
>
> any help is welcome
>
> Juan
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from
> it, send
> an email to raxml+un...@googlegroups.com <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml+un...@googlegroups.com <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com <mailto:raxml%252Buns...@googlegroups.com>>>.
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>
> www.exelixis-lab.org <http://www.exelixis-lab.org> <http://www.exelixis-lab.org>
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>
>
> --
> You received this message because you are subscribed to a topic in
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>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674 <tel:56-63-2221674>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fax: 56-63-2221344 <tel:56-63-2221344>
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y Evolución <http://www.ecolevol.cl>
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com <mailto:raxml%2Bunsu...@googlegroups.com>
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y Evolución <http://www.ecolevol.cl>
>
> --
> You received this message because you are subscribed to the Google
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> To unsubscribe from this group and stop receiving emails from it, send
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> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
> --
> You received this message because you are subscribed to a topic in the Google Groups "raxml" group.
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> <mailto:raxml%2Bunsu...@googlegroups.com>.
> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674 <tel:56-63-2221674>
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
> --
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Juan C. Opazo
Dec 8, 2015, 7:32:27 PM12/8/15
to raxml
Hi Alex, do you mean adding a -T 2 for example? so the command would be:
cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$ raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -N 10 -T 2
cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$ raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -N 10 -T 2
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Juan C. Opazo
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
Alexey Kozlov
Dec 8, 2015, 7:36:32 PM12/8/15
to ra...@googlegroups.com
No, -T parameter is for PTHREADS version only (which you could also try BTW), but if you want to use MPI you'd need
something like:
cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$ mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n
outfile
Alexey
On 09.12.2015 01:32, Juan C. Opazo wrote:
> Hi Alex, do you mean adding a -T 2 for example? so the command would be:
>
> cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$ raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -N 10
> -T 2
>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>
> <mailto:raxml%25252Bun...@googlegroups.com>>>>.
> <mailto:raxml%252Buns...@googlegroups.com <mailto:raxml%25252Bun...@googlegroups.com>>>.
> fax: 56-63-2221344 <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
> fono: 56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674 <tel:56-63-2221674>>
> fax: 56-63-2221344 <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
something like:
cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$ mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n
outfile
Alexey
On 09.12.2015 01:32, Juan C. Opazo wrote:
> Hi Alex, do you mean adding a -T 2 for example? so the command would be:
>
> cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$ raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -N 10
> -T 2
>
> <mailto:raxml%252Buns...@googlegroups.com> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>
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> Alexandros (Alexis) Stamatakis
>
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> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>
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>
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
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> of Arizona at Tucson
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> Universidad Austral de Chile
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> fono: 56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674 <tel:56-63-2221674>>
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> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fax: 56-63-2221344 <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
> jopazo (at) gmail (dot) com
>
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> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y Evolución <http://www.ecolevol.cl>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674 <tel:56-63-2221674>
> fax: 56-63-2221344 <tel:56-63-2221344>
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
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> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
Juan C. Opazo
Dec 8, 2015, 7:45:52 PM12/8/15
to raxml
Bingo! now it works!
thank you very much you all your time!
all the best
juan
cbuach@ubuntu-frontend:~/Desktop/prueba_RAxML$ mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAJTT -n outfile -N 10
This is RAxML MPI Process Number: 0
This is RAxML MPI Process Number: 1
Inference[5]: Time 23.634978 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[0]: Time 23.636933 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[6]: Time 23.568601 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[1]: Time 23.700877 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[7]: Time 23.467421 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[2]: Time 23.379018 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[3]: Time 23.410665 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[8]: Time 23.633969 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[4]: Time 23.364898 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[9]: Time 23.639813 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[0]: Time 23.636933 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[6]: Time 23.568601 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[1]: Time 23.700877 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[7]: Time 23.467421 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[2]: Time 23.379018 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[3]: Time 23.410665 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[8]: Time 23.633969 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[4]: Time 23.364898 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Inference[9]: Time 23.639813 GAMMA-based likelihood -6306.468434, best rearrangement setting 5
Conducting final model optimizations on all 10 trees under GAMMA-based models ....
Inference[5] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.5
Inference[0] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.0
Inference[1] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.1
Inference[1] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.1
Inference[6] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.6
Inference[2] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.2
Inference[7] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.7
Inference[3] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.3
Inference[8] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.8
Inference[4] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.4
Inference[9] final GAMMA-based Likelihood: -6306.468434 tree written to file /home/cbuach/Desktop/prueba_RAxML/RAxML_result.outfile.RUN.9
Starting final GAMMA-based thorough Optimization on tree 9 likelihood -6306.468434 ....
Final GAMMA-based Score of best tree -6306.468434
Program execution info written to /home/cbuach/Desktop/prueba_RAxML/RAxML_info.outfile
Best-scoring ML tree written to: /home/cbuach/Desktop/prueba_RAxML/RAxML_bestTree.outfile
Overall execution time: 126.315319 secs or 0.035088 hours or 0.001462 days
Final GAMMA-based Score of best tree -6306.468434
Program execution info written to /home/cbuach/Desktop/prueba_RAxML/RAxML_info.outfile
Best-scoring ML tree written to: /home/cbuach/Desktop/prueba_RAxML/RAxML_bestTree.outfile
Overall execution time: 126.315319 secs or 0.035088 hours or 0.001462 days
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--
Juan C. Opazo
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
fax: 56-63-2221344
jopazo (at) gmail (dot) com
OpazoLab
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
fax: 56-63-2221344
jopazo (at) gmail (dot) com
OpazoLab
Juan C. Opazo
Dec 8, 2015, 8:08:31 PM12/8/15
to raxml
Hi Alex, one more question I am also defining the command to select the best model for amino acid alignments. At the beginning I used:
raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO --auto-prot=aicc -n outfile -# 2
and I got the model, nothing else.raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO --auto-prot=aicc -n outfile -# 2
mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO --auto-prot=aicc -n outfile -# 2
Alexandros Stamatakis
Dec 9, 2015, 4:56:06 AM12/9/15
to ra...@googlegroups.com
Hi Juan,
Note that Alexey also answered on here (he is my PhD student) so it was
not only me who helped, I admit the names are pretty similar.
Alexey, I've noted that I need to include a check for #processes < 2
> raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> and I got the model, nothing else.
>
> After including the "mpirun -n 2"as you suggested:
>
> mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> I am also obtaining the best tree. Is that ok? the best tree
> reconstruction is using the best model selected?
That should be the case, but I am not 100% sure if this is what the code
does, I will need to check, but it will take some time until I get to this.
Alexis
> <mailto:alexei...@gmail.com
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>>>
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>>>>.
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>>>.
> <tel:56-63-2221674 <tel:56-63-2221674>> <tel:56-63-2221674
Note that Alexey also answered on here (he is my PhD student) so it was
not only me who helped, I admit the names are pretty similar.
Alexey, I've noted that I need to include a check for #processes < 2
> raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> and I got the model, nothing else.
>
> After including the "mpirun -n 2"as you suggested:
>
> mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> I am also obtaining the best tree. Is that ok? the best tree
> reconstruction is using the best model selected?
does, I will need to check, but it will take some time until I get to this.
Alexis
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>>>
>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>
>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>
> <mailto:raxml%252Buns...@googlegroups.com
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> <mailto:raxml%2Bunsu...@googlegroups.com>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>
>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>
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> <mailto:raxml%2525252Bu...@googlegroups.com>>>>>.
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> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>
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> <mailto:raxml%2525252Bu...@googlegroups.com>>>>.
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>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> <tel:56-63-2221674> <tel:56-63-2221674 <tel:56-63-2221674>>
> <tel:56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674
> <tel:56-63-2221674>>>
> fax: 56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344 <tel:56-63-2221344>> <tel:56-63-2221344
> https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> <tel:56-63-2221674> <tel:56-63-2221674 <tel:56-63-2221674>>
> <tel:56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674
> <tel:56-63-2221674>>>
> fax: 56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>>
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate
> <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología
> y Evolución <http://www.ecolevol.cl>
>
> --
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> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate
> <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología
> y Evolución <http://www.ecolevol.cl>
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> fax: 56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344 <tel:56-63-2221344>> <tel:56-63-2221344
> fax: 56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>>
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate
> <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y
> Evolución <http://www.ecolevol.cl>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674 <tel:56-63-2221674>
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate
> <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y
> Evolución <http://www.ecolevol.cl>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674 <tel:56-63-2221674>
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> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674 <tel:56-63-2221674>
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> For more options, visit https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674 <tel:56-63-2221674>
Juan C. Opazo
Dec 9, 2015, 6:51:26 AM12/9/15
to raxml
you are right, the names are similar, but anyways, thank you to both of you for helping me with my questions.
bestTo unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
--
Juan C. Opazo
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
Juan C. Opazo
Dec 26, 2015, 3:21:58 PM12/26/15
to raxml
Dear Alex, I have the following question, I ran the bootstrap analysis and when I am tried to get the consensus tree using the this command:
mpirun -n 2 raxmlHPC-MPI -m PROTGAMMAJTT -J MR -z RAxML_bootstrap.outfile -n con
I got this message:mpirun -n 2 raxmlHPC-MPI -m PROTGAMMAJTT -J MR -z RAxML_bootstrap.outfile -n con
This is RAxML MPI Process Number: 0
Error: you are running the parallel MPI program but only want to compute one tree
For the MPI version you must specify a number of trees greater than 1 with the -# or -N option
For the MPI version you must specify a number of trees greater than 1 with the -# or -N option
This is RAxML MPI Process Number: 1
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
I tried changing the -n to 1, but I got the same message, also if I remove the first portion of the command ( mpirun -n 2).mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
Do you have any idea of what is going on?
thank you in advance
Juan
Alexandros Stamatakis
Dec 27, 2015, 1:20:04 AM12/27/15
to ra...@googlegroups.com
you just need to run the consensus option with the sequential or
pthreads version of raxml, the MPI version does not support this,
alexis
On 26.12.2015 21:21, Juan C. Opazo wrote:
> Dear Alex, I have the following question, I ran the bootstrap analysis
> and when I am tried to get the consensus tree using the this command:
>
> mpirun -n 2 raxmlHPC-MPI -m PROTGAMMAJTT -J MR -z
> RAxML_bootstrap.outfile -n con
>
> I got this message:
>
> *This is RAxML MPI Process Number: 0
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>
>
> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>>>>>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>
>
> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>>>>>>.
> <mailto:raxml%2525252Bu...@googlegroups.com>
>
> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>>>>>.
> <tel:56-63-2221674 <tel:56-63-2221674>>> <tel:56-63-2221674
pthreads version of raxml, the MPI version does not support this,
alexis
On 26.12.2015 21:21, Juan C. Opazo wrote:
> Dear Alex, I have the following question, I ran the bootstrap analysis
> and when I am tried to get the consensus tree using the this command:
>
> mpirun -n 2 raxmlHPC-MPI -m PROTGAMMAJTT -J MR -z
> RAxML_bootstrap.outfile -n con
>
> I got this message:
>
> Error: you are running the parallel MPI program but only want to compute
> one tree
> For the MPI version you must specify a number of trees greater than 1
> with the -# or -N option
>
> This is RAxML MPI Process Number: 1
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> --------------------------------------------------------------------------*
> one tree
> For the MPI version you must specify a number of trees greater than 1
> with the -# or -N option
>
> This is RAxML MPI Process Number: 1
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
>
> I tried changing the -n to 1, but I got the same message, also if I
> remove the first portion of the command ( mpirun -n 2).
>
> Do you have any idea of what is going on?
>
> thank you in advance
>
> Juan
>
> On Wed, Dec 9, 2015 at 3:51 AM, Juan C. Opazo <jop...@gmail.com
> <mailto:jop...@gmail.com>> wrote:
>
> you are right, the names are similar, but anyways, thank you to both
> of you for helping me with my questions.
>
> best
>
> juan
>
> On Wed, Dec 9, 2015 at 6:56 AM, Alexandros Stamatakis
> <alexandros...@gmail.com
> I tried changing the -n to 1, but I got the same message, also if I
> remove the first portion of the command ( mpirun -n 2).
>
> Do you have any idea of what is going on?
>
> thank you in advance
>
> Juan
>
> On Wed, Dec 9, 2015 at 3:51 AM, Juan C. Opazo <jop...@gmail.com
> <mailto:jop...@gmail.com>> wrote:
>
> you are right, the names are similar, but anyways, thank you to both
> of you for helping me with my questions.
>
> best
>
> juan
>
> On Wed, Dec 9, 2015 at 6:56 AM, Alexandros Stamatakis
> <alexandros...@gmail.com
> Note that Alexey also answered on here (he is my PhD student) so
> it was not only me who helped, I admit the names are pretty similar.
>
> Alexey, I've noted that I need to include a check for #processes < 2
>
> raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> and I got the model, nothing else.
>
> After including the "mpirun -n 2"as you suggested:
>
> mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m
> PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> I am also obtaining the best tree. Is that ok? the best tree
> reconstruction is using the best model selected?
>
>
> That should be the case, but I am not 100% sure if this is what
> the code does, I will need to check, but it will take some time
> until I get to this.
>
> Alexis
>
>
> best
>
> juan
>
>
> On Tue, Dec 8, 2015 at 9:45 PM, Juan C. Opazo
> <jop...@gmail.com <mailto:jop...@gmail.com>
> it was not only me who helped, I admit the names are pretty similar.
>
> Alexey, I've noted that I need to include a check for #processes < 2
>
> raxmlHPC-MPI -s Alignment.fasta -p 12345 -m PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> and I got the model, nothing else.
>
> After including the "mpirun -n 2"as you suggested:
>
> mpirun -n 2 raxmlHPC-MPI -s Alignment.fasta -p 12345 -m
> PROTGAMMAAUTO
> --auto-prot=aicc -n outfile -# 2
>
> I am also obtaining the best tree. Is that ok? the best tree
> reconstruction is using the best model selected?
>
>
> That should be the case, but I am not 100% sure if this is what
> the code does, I will need to check, but it will take some time
> until I get to this.
>
> Alexis
>
>
> best
>
> juan
>
>
> On Tue, Dec 8, 2015 at 9:45 PM, Juan C. Opazo
> <jop...@gmail.com <mailto:jop...@gmail.com>
> <mailto:raxml%2525252Bu...@googlegroups.com>
>
> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>>>>>
> <mailto:raxml%2525252Bu...@googlegroups.com>
>
> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>>>>>>.
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>>
>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>
>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>>
>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>
>
> <mailto:raxml%2525252Bu...@googlegroups.com>
>
> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>>>>>.
> For more options, visit
> https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs.
> Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>>
> <tel:56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674
> <tel:56-63-2221674>>>
> <tel:56-63-2221674 <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>> <tel:56-63-2221674
> <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>>>>
> https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs.
> Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>>
> <tel:56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674
> <tel:56-63-2221674>>>
> <tel:56-63-2221674 <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>> <tel:56-63-2221674
> <tel:56-63-2221674>
> fax: 56-63-2221344
> <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344 <tel:56-63-2221344>>> <tel:56-63-2221344
> <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221674>
> <tel:56-63-2221674 <tel:56-63-2221674>>
> <tel:56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674
> <tel:56-63-2221674>>>>
> fax: 56-63-2221344
> <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344 <tel:56-63-2221344>>> <tel:56-63-2221344
> <tel:56-63-2221674 <tel:56-63-2221674>>
> <tel:56-63-2221674 <tel:56-63-2221674> <tel:56-63-2221674
> <tel:56-63-2221674>>>>
> fax: 56-63-2221344
> <tel:56-63-2221344> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344>
> <tel:56-63-2221344>
> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344> <tel:56-63-2221344
> <tel:56-63-2221344 <tel:56-63-2221344>>
> <tel:56-63-2221344 <tel:56-63-2221344> <tel:56-63-2221344
> <tel:56-63-2221344>>>>
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate
> <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención
> Ecología y
> Evolución <http://www.ecolevol.cl>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> <tel:56-63-2221674> <tel:56-63-2221674 <tel:56-63-2221674>>
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate
> <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención
> Ecología y
> Evolución <http://www.ecolevol.cl>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> <tel:56-63-2221674> <tel:56-63-2221674 <tel:56-63-2221674>>
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of
> Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of
> Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
>
Juan C. Opazo
Dec 27, 2015, 4:20:26 AM12/27/15
to ra...@googlegroups.com
Ok, thank you for your answer.
Best
Juan
Sent from my interior
> To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
Best
Juan
Sent from my interior
Juan C. Opazo
Dec 28, 2015, 7:00:56 AM12/28/15
to raxml
Dear Alex, its me again, I installed RAxML from the repository and I made the consensus tree using the following instructions:
raxmlHPC -m PROTGAMMAJTT -J MR -z RAxML_bootstrap.outfile -n con
I got the following output:raxmlHPC -m PROTGAMMAJTT -J MR -z RAxML_bootstrap.outfile -n con
_________________________________________________________________
Found a total of 118 taxa in first tree of tree collection RAxML_bootstrap.outfile
Expecting all remaining trees in collection to have the same taxon set
This is RAxML version 7.2.8 released by Alexandros Stamatakis in October 2010.
Found a total of 118 taxa in first tree of tree collection RAxML_bootstrap.outfile
Expecting all remaining trees in collection to have the same taxon set
This is RAxML version 7.2.8 released by Alexandros Stamatakis in October 2010.
With greatly appreciated code contributions by:
Andre Aberer (TUM)
Simon Berger (TUM)
John Cazes (TACC)
Michael Ott (TUM)
Nick Pattengale (UNM)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (Univ. Tsukuba)
RAxML consensus tree computation
Simon Berger (TUM)
John Cazes (TACC)
Michael Ott (TUM)
Nick Pattengale (UNM)
Wayne Pfeiffer (SDSC)
Akifumi S. Tanabe (Univ. Tsukuba)
RAxML consensus tree computation
RAxML was called as follows:
raxmlHPC -m PROTGAMMAJTT -J MR -z RAxML_bootstrap.outfile -n con
Found 1008 trees in File RAxML_bootstrap.outfile
RAxML Majority Rule consensus tree written to file: XXXXXXXXXX/RAxML_MajorityRuleConsensusTree.con
_________________________________________________________________
Found 1008 trees in File RAxML_bootstrap.outfile
RAxML Majority Rule consensus tree written to file: XXXXXXXXXX/RAxML_MajorityRuleConsensusTree.con
_________________________________________________________________
Finally I tried to open the tree in FigTree but I got this error message:
Error reading the tree file
Number Format Error: For input string : "1.0[97]"
do you have an idea of what is going on?
thank you in advance
juan
Alexandros Stamatakis
Dec 28, 2015, 9:23:00 AM12/28/15
to ra...@googlegroups.com
hi juan,
1. you should update to raxml version 8.2.4 available at:
https://github.com/stamatak/standard-RAxML
2. the dendroscope viewer can correctly read this output format
alexis
> >> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>
> >> <mailto:raxml%252525252B...@googlegroups.com
> <mailto:raxml%25252525252...@googlegroups.com>>>>>>
> >> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>
> >> <mailto:raxml%252525252B...@googlegroups.com
> <mailto:raxml%25252525252...@googlegroups.com>>>>>>>.
> >> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>
> >> <mailto:raxml%252525252B...@googlegroups.com
> <mailto:raxml%25252525252...@googlegroups.com>>>>>>.
> >> an email toraxml+u...@googlegroups.com
1. you should update to raxml version 8.2.4 available at:
https://github.com/stamatak/standard-RAxML
2. the dendroscope viewer can correctly read this output format
alexis
> >> <mailto:jop...@gmail.com <mailto:jop...@gmail.com>>> wrote:
> >>
> >> you are right, the names are similar, but anyways, thank you
> to both
> >> of you for helping me with my questions.
> >>
> >> best
> >>
> >> juan
> >>
> >> On Wed, Dec 9, 2015 at 6:56 AM, Alexandros Stamatakis
> >> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> >>
> >> you are right, the names are similar, but anyways, thank you
> to both
> >> of you for helping me with my questions.
> >>
> >> best
> >>
> >> juan
> >>
> >> On Wed, Dec 9, 2015 at 6:56 AM, Alexandros Stamatakis
> >> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> >> <mailto:alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>>> wrote:
> >>
> >> Hi Juan,
> >>
> <mailto:alexandros...@gmail.com>>> wrote:
> >>
> >> Hi Juan,
> >>
> <mailto:raxml%252525252B...@googlegroups.com>
> >> <mailto:raxml%252525252B...@googlegroups.com
> <mailto:raxml%25252525252...@googlegroups.com>>>>>>
> <mailto:raxml%252525252B...@googlegroups.com>
> >> <mailto:raxml%252525252B...@googlegroups.com
> <mailto:raxml%25252525252...@googlegroups.com>>>>>>>.
> <mailto:raxml%252525252B...@googlegroups.com>
> >> <mailto:raxml%252525252B...@googlegroups.com
> <mailto:raxml%25252525252...@googlegroups.com>>>>>>.
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> >> <tel:56-63-2221344 <tel:56-63-2221344>>
> >> jopazo (at) gmail (dot) com
> >>
> >> OpazoLab <http://www.opazolab.cl/>
> >> ResearchGate
> >> <https://www.researchgate.net/profile/Juan_Opazo>
> >> Doctorado en Ciencias mención Ecología y Evolución
> >> <http://www.ecolevol.cl>
> >>
> >> --
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> >> <tel:56-63-2221344 <tel:56-63-2221344>>
> >> jopazo (at) gmail (dot) com
> >>
> >> OpazoLab <http://www.opazolab.cl/>
> >> ResearchGate
> >> <https://www.researchgate.net/profile/Juan_Opazo>
> >> Doctorado en Ciencias mención Ecología y Evolución
> >> <http://www.ecolevol.cl>
> >>
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> <mailto:raxml%252Buns...@googlegroups.com>
> >> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>
> >>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> >> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> >>
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> <mailto:raxml%252Buns...@googlegroups.com>
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> >> toraxml+u...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> >> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>
> >>
> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> >> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> >>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> >> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>>.
> >> For more options, visit
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> >> --
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> >> To unsubscribe from this group and all its topics,
> >> send an email
> >> Juan C. Opazo
> >> Instituto de Cs. Ambientales y Evolutivas
> >> Facultad de Ciencias
> >> Universidad Austral de Chile
> >> Casilla 567, Valdivia
> >> Chile
> >> fono: 56-63-2221674 <tel:56-63-2221674>
> >> fax: 56-63-2221344 <tel:56-63-2221344>
> >> jopazo (at) gmail (dot) com
> >>
> >> OpazoLab <http://www.opazolab.cl/>
> >> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> >> Doctorado en Ciencias mención Ecología y Evolución
> >> <http://www.ecolevol.cl>
> >>
> >> --
> >> You received this message because you are subscribed to the
> >> Google
> >> Groups "raxml" group.
> >> To unsubscribe from this group and stop receiving emails
> >> from it, send
> >> an email toraxml+u...@googlegroups.com
> >> Instituto de Cs. Ambientales y Evolutivas
> >> Facultad de Ciencias
> >> Universidad Austral de Chile
> >> Casilla 567, Valdivia
> >> Chile
> >> fono: 56-63-2221674 <tel:56-63-2221674>
> >> fax: 56-63-2221344 <tel:56-63-2221344>
> >> jopazo (at) gmail (dot) com
> >>
> >> OpazoLab <http://www.opazolab.cl/>
> >> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> >> Doctorado en Ciencias mención Ecología y Evolución
> >> <http://www.ecolevol.cl>
> >>
> >> --
> >> You received this message because you are subscribed to the
> >> Groups "raxml" group.
> >> To unsubscribe from this group and stop receiving emails
> >> from it, send
> <mailto:raxml%2Bunsu...@googlegroups.com>
> >> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> >> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> >> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>>.
> >> For more options, visithttps://groups.google.com/d/optout.
> >> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> >> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> >> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>>.
> >>
> >>
> >> --
> >> Alexandros (Alexis) Stamatakis
> >>
> >> Research Group Leader, Heidelberg Institute for Theoretical Studies
> >> Full Professor, Dept. of Informatics, Karlsruhe Institute of
> >> Technology
> >> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> >> University
> >> of Arizona at Tucson
> >>
> >>www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org>
> >>
> >>
> >> --
> >> Alexandros (Alexis) Stamatakis
> >>
> >> Research Group Leader, Heidelberg Institute for Theoretical Studies
> >> Full Professor, Dept. of Informatics, Karlsruhe Institute of
> >> Technology
> >> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> >> University
> >> of Arizona at Tucson
> >>
> >>www.exelixis-lab.org <http://www.exelixis-lab.org>
> <http://www.exelixis-lab.org>
> >>
> >> --
> >> You received this message because you are subscribed to a topic
> >> in the Google Groups "raxml" group.
> >> To unsubscribe from this topic, visit
> >>https://groups.google.com/d/topic/raxml/xh8DcOMULHw/unsubscribe.
> >> To unsubscribe from this group and all its topics, send an email
> >> toraxml+u...@googlegroups.com
> >> You received this message because you are subscribed to a topic
> >> in the Google Groups "raxml" group.
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> >>https://groups.google.com/d/topic/raxml/xh8DcOMULHw/unsubscribe.
> >> To unsubscribe from this group and all its topics, send an email
> <mailto:raxml%2Bunsu...@googlegroups.com>
> >> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>.
> >> For more options, visithttps://groups.google.com/d/optout.
> >> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>.
> <mailto:raxml%2Bunsu...@googlegroups.com>
> >> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> >> For more options, visithttps://groups.google.com/d/optout.
> >> <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> >
> > --
> > Alexandros (Alexis) Stamatakis
> >
> > Research Group Leader, Heidelberg Institute for Theoretical Studies
> > Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> > Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> > of Arizona at Tucson
> >
> >www.exelixis-lab.org <http://www.exelixis-lab.org>
> >
> > --
> > You received this message because you are subscribed to a topic in the Google Groups "raxml" group.
> > To unsubscribe from this topic, visithttps://groups.google.com/d/topic/raxml/xh8DcOMULHw/unsubscribe.
> > --
> > Alexandros (Alexis) Stamatakis
> >
> > Research Group Leader, Heidelberg Institute for Theoretical Studies
> > Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> > Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> > of Arizona at Tucson
> >
> >www.exelixis-lab.org <http://www.exelixis-lab.org>
> >
> > --
> > You received this message because you are subscribed to a topic in the Google Groups "raxml" group.
> > To unsubscribe from this group and all its topics, send an email
> to raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>.
> > For more options, visit https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> to raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>.
> > For more options, visit https://groups.google.com/d/optout.
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
Juan C. Opazo
Dec 28, 2015, 4:49:15 PM12/28/15
to raxml
It works! thank you very much!
--
Juan C. Opazo
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
fax: 56-63-2221344
jopazo (at) gmail (dot) com
OpazoLab
Instituto de Cs. Ambientales y Evolutivas
Facultad de Ciencias
Universidad Austral de Chile
Casilla 567, Valdivia
Chile
fono: 56-63-2221674
fax: 56-63-2221344
jopazo (at) gmail (dot) com
OpazoLab
Juan C. Opazo
Jan 20, 2016, 7:39:48 AM1/20/16
to raxml
Hi Alex, I have a question for you regarding the-i parameter. You mention that the value of this parameter is determine automatically by raxml, but it is possible to know the value assigned? Can you guide me regarding the values should I use? I guess a higher number means that the exploration of the tree space is better? Am I right?
thank you in advanceAlexandros Stamatakis
Jan 21, 2016, 4:09:39 AM1/21/16
to ra...@googlegroups.com
On 20.01.2016 13:39, Juan C. Opazo wrote:
> Hi Alex, I have a question for you regarding the-i parameter. You
> mention that the value of this parameter is determine automatically by
> raxml, but it is possible to know the value assigned?
radius" or something similar ...
> Can you guide me
> regarding the values should I use?
> I guess a higher number means that
> the exploration of the tree space is better? Am I right?
alexis
>
> thank you in advance
>
> juan
>
> On Mon, Dec 28, 2015 at 6:48 PM, Juan C. Opazo <jop...@gmail.com
> <mailto:jop...@gmail.com>> wrote:
>
> It works! thank you very much!
>
> On Mon, Dec 28, 2015 at 6:22 AM, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:jop...@gmail.com <mailto:jop...@gmail.com>>> wrote:
>
> Ok, thank you for your answer.
>
> Best
>
> Juan
>
> Sent from my interior
>
> > On Dec 27, 2015, at 3:19 AM, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
>
> Ok, thank you for your answer.
>
> Best
>
> Juan
>
> Sent from my interior
>
> > On Dec 27, 2015, at 3:19 AM, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> >> <mailto:jop...@gmail.com <mailto:jop...@gmail.com>
> <mailto:jop...@gmail.com <mailto:jop...@gmail.com>>>> wrote:
> >>
> >> you are right, the names are similar, but
> anyways, thank you
> to both
> >> of you for helping me with my questions.
> >>
> >> best
> >>
> >> juan
> >>
> >> On Wed, Dec 9, 2015 at 6:56 AM, Alexandros
> Stamatakis
> >> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> <mailto:alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>>
> <mailto:jop...@gmail.com <mailto:jop...@gmail.com>>>> wrote:
> >>
> >> you are right, the names are similar, but
> anyways, thank you
> to both
> >> of you for helping me with my questions.
> >>
> >> best
> >>
> >> juan
> >>
> >> On Wed, Dec 9, 2015 at 6:56 AM, Alexandros
> Stamatakis
> >> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> <mailto:alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>>
> >> <mailto:alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> <mailto:alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>>>> wrote:
> >>
> >> Hi Juan,
> >>
> <mailto:alexandros...@gmail.com>
> <mailto:alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>>>> wrote:
> >>
> >> Hi Juan,
> >>
> >>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>
> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>>>>>
> >>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>
> >>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>>
> >>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>
> <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>
> >>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>>
> >>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> >>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>
> <mailto:raxml%2525252Bu...@googlegroups.com
> <mailto:raxml%252525252B...@googlegroups.com>>>>
> >>
> >>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>
> >>
> <mailto:raxml%25252Bun...@googlegroups.com
> >>
> <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>
> <mailto:raxml%25252Bun...@googlegroups.com
> <mailto:raxml%2525252Bu...@googlegroups.com>>
> >>
> <mailto:raxml%2525252Bu...@googlegroups.com>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674 <tel:56-63-2221674>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fax: 56-63-2221344 <tel:56-63-2221344>
> jopazo (at) gmail (dot) com
>
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y Evolución
> <http://www.ecolevol.cl>
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> fax: 56-63-2221344
> jopazo (at) gmail (dot) com
>
>
>
>
> --
> Juan C. Opazo
> Instituto de Cs. Ambientales y Evolutivas
> Facultad de Ciencias
> Universidad Austral de Chile
> Casilla 567, Valdivia
> Chile
> fono: 56-63-2221674
> fax: 56-63-2221344
> jopazo (at) gmail (dot) com
>
> OpazoLab <http://www.opazolab.cl/>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
> Doctorado en Ciencias mención Ecología y Evolución <http://www.ecolevol.cl>
> ResearchGate <https://www.researchgate.net/profile/Juan_Opazo>
>
> --
> You received this message because you are subscribed to the Google
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> To unsubscribe from this group and stop receiving emails from it, send
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