Choosing the best tree from the OUT file
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SUNITHA
Nov 11, 2016, 4:35:06 AM11/11/16
to raxml
I have called RaxMLHPC MPI as follows
mpiexec -np 32 /share/apps/bio/RAxML/raxmlHPC-MPI-SSE3 -f d -m GTRCAT -s /home/my_alignment.phylip -n my_file.out -p $RANDOM -b $RANDOM -N 500
Got an OUT file - RAxML_bootstrap.my_file.out
Overall Time for 504 Bootstraps 336001.156673
Average Time per Bootstrap 666.668962
All 504 bootstrapped trees written to: /home/sp/RAxML_bootstrap.my_file.out
How to get the best tree from these 504 trees? Could someone help me please?
Thanks in advance!
Christian Cramer
Nov 11, 2016, 5:15:58 AM11/11/16
to ra...@googlegroups.com
Hi Sunitha,
there should be a file like RAxML_bestTree.my_file
Add the file-extension .tre and you have your best tree
Bests,
Christian
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Alexandros Stamatakis
Nov 11, 2016, 9:28:40 AM11/11/16
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sunitha,
the command line you indicated will only generate bootstrap tree
replicates, so there is no reason to expect RAxML to calculate a
best-known ML tree on the original alignment for this command,
alexis
On 11.11.2016 11:15, 'Christian Cramer' via raxml wrote:
> Hi Sunitha,
>
> there should be a file like RAxML_bestTree.my_file
> Add the file-extension .tre and you have your best tree
>
> Bests,
> Christian
>
> 2016-11-11 10:35 GMT+01:00 SUNITHA <suni...@gmail.com
> <mailto:suni...@gmail.com>>:
> <mailto:raxml+un...@googlegroups.com>.
> <mailto:raxml+un...@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
the command line you indicated will only generate bootstrap tree
replicates, so there is no reason to expect RAxML to calculate a
best-known ML tree on the original alignment for this command,
alexis
On 11.11.2016 11:15, 'Christian Cramer' via raxml wrote:
> Hi Sunitha,
>
> there should be a file like RAxML_bestTree.my_file
> Add the file-extension .tre and you have your best tree
>
> Bests,
> Christian
>
> 2016-11-11 10:35 GMT+01:00 SUNITHA <suni...@gmail.com
>
>
>
> I have called RaxMLHPC MPI as follows
>
> mpiexec -np 32 /share/apps/bio/RAxML/raxmlHPC-MPI-SSE3 -f d -m
> GTRCAT -s /home/my_alignment.phylip -n my_file.out -p $RANDOM -b
> $RANDOM -N 500
>
>
> Got an OUT file - RAxML_bootstrap.my_file.out
>
> Overall Time for 504 Bootstraps 336001.156673
> Average Time per Bootstrap 666.668962
> All 504 bootstrapped trees written to:
> /home/sp/RAxML_bootstrap.my_file.out
>
> How to get the best tree from these 504 trees? Could someone help me
> please?
>
>
> Thanks in advance!
>
> --
> 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
>
>
> I have called RaxMLHPC MPI as follows
>
> mpiexec -np 32 /share/apps/bio/RAxML/raxmlHPC-MPI-SSE3 -f d -m
> GTRCAT -s /home/my_alignment.phylip -n my_file.out -p $RANDOM -b
> $RANDOM -N 500
>
>
> Got an OUT file - RAxML_bootstrap.my_file.out
>
> Overall Time for 504 Bootstraps 336001.156673
> Average Time per Bootstrap 666.668962
> All 504 bootstrapped trees written to:
> /home/sp/RAxML_bootstrap.my_file.out
>
> How to get the best tree from these 504 trees? Could someone help me
> please?
>
>
> Thanks in advance!
>
> --
> You received this message because you are subscribed to the Google
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>
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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
SUNITHA P
Nov 12, 2016, 3:37:16 AM11/12/16
to ra...@googlegroups.com
Thank you Christian & Alexis for your reply.
@ Christian, no such file was generated.
@ Alexis,
Could you please help me to modify the code, so as to get the best tree after bootstrapping.
Do I need to re-run the program or is there any way out to calculate the best tree from the bootstrap replicates, already got?
If I need to re-run, how should I modify the code?
Please help me out.
Best
Sunitha
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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
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Alexandros Stamatakis
Nov 12, 2016, 6:45:30 AM11/12/16
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On 12.11.2016 09:36, SUNITHA P wrote:
> Thank you Christian & Alexis for your reply.
>
> @ Christian, no such file was generated.
>
> @ Alexis,
> Could you please help me to modify the code, so as to get the best tree
> after bootstrapping.
> Do I need to re-run the program or is there any way out to calculate the
> best tree from the bootstrap replicates, already got?
> If I need to re-run, how should I modify the code?
http://sco.h-its.org/exelixis/resource/download/NewManual.pdf
and at the step by step tutorial:
http://sco.h-its.org/exelixis/web/software/raxml/hands_on.html
alexis
>
> Please help me out.
>
> Best
>
> Sunitha
>
> On Fri, Nov 11, 2016 at 7:58 PM, Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> sunitha,
>
> the command line you indicated will only generate bootstrap tree
> replicates, so there is no reason to expect RAxML to calculate a
> best-known ML tree on the original alignment for this command,
>
> alexis
>
> On 11.11.2016 11:15, 'Christian Cramer' via raxml wrote:
>
> Hi Sunitha,
>
> there should be a file like RAxML_bestTree.my_file
> Add the file-extension .tre and you have your best tree
>
> Bests,
> Christian
>
> 2016-11-11 10:35 GMT+01:00 SUNITHA <suni...@gmail.com
> <mailto:suni...@gmail.com>
> <mailto:suni...@gmail.com <mailto:suni...@gmail.com>>>:
>
> sunitha,
>
> the command line you indicated will only generate bootstrap tree
> replicates, so there is no reason to expect RAxML to calculate a
> best-known ML tree on the original alignment for this command,
>
> alexis
>
> On 11.11.2016 11:15, 'Christian Cramer' via raxml wrote:
>
> Hi Sunitha,
>
> there should be a file like RAxML_bestTree.my_file
> Add the file-extension .tre and you have your best tree
>
> Bests,
> Christian
>
> 2016-11-11 10:35 GMT+01:00 SUNITHA <suni...@gmail.com
> <mailto:suni...@gmail.com>
>
>
>
> I have called RaxMLHPC MPI as follows
>
> mpiexec -np 32 /share/apps/bio/RAxML/raxmlHPC-MPI-SSE3 -f d -m
> GTRCAT -s /home/my_alignment.phylip -n my_file.out -p $RANDOM -b
> $RANDOM -N 500
>
>
> Got an OUT file - RAxML_bootstrap.my_file.out
>
> Overall Time for 504 Bootstraps 336001.156673
> Average Time per Bootstrap 666.668962
> All 504 bootstrapped trees written to:
> /home/sp/RAxML_bootstrap.my_file.out
>
> How to get the best tree from these 504 trees? Could someone
> help me
> please?
>
>
> Thanks in advance!
>
> --
> 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
>
>
> I have called RaxMLHPC MPI as follows
>
> mpiexec -np 32 /share/apps/bio/RAxML/raxmlHPC-MPI-SSE3 -f d -m
> GTRCAT -s /home/my_alignment.phylip -n my_file.out -p $RANDOM -b
> $RANDOM -N 500
>
>
> Got an OUT file - RAxML_bootstrap.my_file.out
>
> Overall Time for 504 Bootstraps 336001.156673
> Average Time per Bootstrap 666.668962
> All 504 bootstrapped trees written to:
> /home/sp/RAxML_bootstrap.my_file.out
>
> How to get the best tree from these 504 trees? Could someone
> help me
> please?
>
>
> Thanks in advance!
>
> --
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>
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>
> --
> <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>
>
> 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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