Partitioned analysis whit models for each one
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SANTIAGO OROZCO CHAMORRO
Dec 15, 2017, 5:00:37 PM12/15/17
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HI
I have been trying to run RAxML HPC2 on XSEDE on CIPRES whit my dataset, which have a gene (600 bp) and partitions by codon. The partition scheme and the best models for each one were calculated in Partitionfinder. I ran a analysis putting in the option “Used a mixed/partitioned model” a file with looks like:
DNA, Subset1 = 1-677\3
DNA, Subset2 = 2-677\3
DNA, Subset3 = 3-677\3
It works well, but I want put the model that partitionfinder found for each codon. In the advanced parametes I want change the number of alternatives runs but it don’t let me do it. Bootstrap iterations = 1000.
Thanks for help me!
Fidel Botero
Dec 16, 2017, 10:34:53 AM12/16/17
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Hola Santiago,
This is not possible in RaxML. What will be done is that the model you specify with -m will be fitted for each partition.
My suggestion would thus be running the analysis under the most general model you found with PartitionModel.
Hoping this helps you.
Best,
Fidel
--Hacia una Universidad comprometida con la Paz Territorial
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SANTIAGO OROZCO CHAMORRO
Dec 16, 2017, 2:00:45 PM12/16/17
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Hi Fidel
Thanks for you help. I will try to use PartitionModel and run the RAxML.
If you know....I have a bayesian tree built whit the partition and model for each one, can I compare this tree whit ML tree built whitout model for each partition?
Thanks again!
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Atentamente,
SANTIAGO OROZCO CHAMORRO
Estudiante de Biología
Universidad del Cauca
Alexandros Stamatakis
Dec 17, 2017, 7:13:28 AM12/17/17
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Thanks Fidel :-)
Santiago: if you want to use exactly the model found by Partitionfinder
please switch to the new RAxML-NG that is more flexible model-wise:
https://github.com/amkozlov/raxml-ng
You can compare trees inferred under slightly different models and using
different inference methods, but you need to make sure to highlight that
the models were different. So in the end you will not be able to
determine if the differences are due to (i) a different model or (ii) a
distinct tree inference method.
Alexis
On 16.12.2017 20:00, SANTIAGO OROZCO CHAMORRO wrote:
> Hi Fidel
>
> Thanks for you help. I will try to use PartitionModel and run the RAxML.
>
> If you know....I have a bayesian tree built whit the partition and model
> for each one, can I compare this tree whit ML tree built whitout model
> for each partition?
>
> Thanks again!
>
> 2017-12-16 10:34 GMT-05:00 Fidel Botero <fidel....@gmail.com
> <mailto:fidel....@gmail.com>>:
>
> HI____
>
> __ __
>
> DNA, Subset1 = 1-677\3____
>
> DNA, Subset2 = 2-677\3 ____
>
> DNA, Subset3 = 3-677\3____
>
> __ __
>
> Thanks for help me!____
>
>
> ------------------------------------------------------------------------
>
> /Hacia una Universidad comprometida con la Paz Territorial/
> <mailto:raxml+un...@googlegroups.com>.
> <mailto:raxml+un...@googlegroups.com>.
>
>
>
>
> --
> Atentamente,
>
>
> *_SANTIAGO OROZCO CHAMORRO _*
> / Estudiante de Biología/
> /Universidad del //Cauca/
> //
>
> ------------------------------------------------------------------------
>
> /Hacia una Universidad comprometida con la Paz Territorial/
> <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
www.exelixis-lab.org
Santiago: if you want to use exactly the model found by Partitionfinder
please switch to the new RAxML-NG that is more flexible model-wise:
https://github.com/amkozlov/raxml-ng
You can compare trees inferred under slightly different models and using
different inference methods, but you need to make sure to highlight that
the models were different. So in the end you will not be able to
determine if the differences are due to (i) a different model or (ii) a
distinct tree inference method.
Alexis
On 16.12.2017 20:00, SANTIAGO OROZCO CHAMORRO wrote:
> Hi Fidel
>
> Thanks for you help. I will try to use PartitionModel and run the RAxML.
>
> If you know....I have a bayesian tree built whit the partition and model
> for each one, can I compare this tree whit ML tree built whitout model
> for each partition?
>
> Thanks again!
>
> 2017-12-16 10:34 GMT-05:00 Fidel Botero <fidel....@gmail.com
>
> Hola Santiago,
> This is not possible in RaxML. What will be done is that the model
> you specify with -m will be fitted for each partition.
> My suggestion would thus be running the analysis under the most
> general model you found with PartitionModel.
>
> Hoping this helps you.
>
> Best,
>
> Fidel
>
> El 15 dic. 2017 11:00 PM, "SANTIAGO OROZCO CHAMORRO"
> <sor...@unicauca.edu.co <mailto:sor...@unicauca.edu.co>> escribió:
> Hola Santiago,
> This is not possible in RaxML. What will be done is that the model
> you specify with -m will be fitted for each partition.
> My suggestion would thus be running the analysis under the most
> general model you found with PartitionModel.
>
> Hoping this helps you.
>
> Best,
>
> Fidel
>
> El 15 dic. 2017 11:00 PM, "SANTIAGO OROZCO CHAMORRO"
>
> HI____
>
> I have been trying to run RAxML HPC2 on XSEDE on CIPRES whit my
> dataset, which have a gene (600 bp) and partitions by codon. The
> partition scheme and the best models for each one were
> calculated in Partitionfinder. I ran a analysis putting in the
> option “Used a mixed/partitioned model” a file with looks like:____
> I have been trying to run RAxML HPC2 on XSEDE on CIPRES whit my
> dataset, which have a gene (600 bp) and partitions by codon. The
> partition scheme and the best models for each one were
> calculated in Partitionfinder. I ran a analysis putting in the
>
> __ __
>
> DNA, Subset1 = 1-677\3____
>
> DNA, Subset2 = 2-677\3 ____
>
> DNA, Subset3 = 3-677\3____
>
> __ __
>
> It works well, but I want put the model that partitionfinder
> found for each codon. In the advanced parametes I want change
> the number of alternatives runs but it don’t let me do it.
> Bootstrap iterations = 1000.____
> It works well, but I want put the model that partitionfinder
> found for each codon. In the advanced parametes I want change
> the number of alternatives runs but it don’t let me do it.
>
> Thanks for help me!____
>
>
> ------------------------------------------------------------------------
>
> /Hacia una Universidad comprometida con la Paz Territorial/
>
> --
> 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
> --
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>
>
>
>
> --
> Atentamente,
>
>
> *_SANTIAGO OROZCO CHAMORRO _*
> / Estudiante de Biología/
> /Universidad del //Cauca/
> //
>
> ------------------------------------------------------------------------
>
> /Hacia una Universidad comprometida con la Paz Territorial/
>
> --
> 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
> --
> You received this message because you are subscribed to the Google
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> <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
www.exelixis-lab.org
SANTIAGO OROZCO CHAMORRO
Jan 22, 2018, 12:23:37 PM1/22/18
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Hello Alexandros And fidel
Thanks for answer to my questions. it was of great help for me! Good day
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Atentamente,
*_SANTIAGO OROZCO CHAMORRO _*
/ Estudiante de Biología/
/Universidad del //Cauca/
//
------------------------------------------------------------------------
/Hacia una Universidad comprometida con la Paz Territorial/
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--
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
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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Atentamente,
SANTIAGO OROZCO CHAMORRO
Estudiante de Biología
Universidad del Cauca
Hacia una Universidad comprometida con la Paz Territorial
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