Defining Populations in RAxML

[cav...@gmail.com]

I ran the following code for RAxML and instead of getting a tree for the populations or individuals it gave me a tree for each locus for each sample.  I want know how to define the populations so that I can run a tree that shows how the populations are related.

The alignment fasta file alignment.fasta look like this:

>CLocus_2130_Sample_581_Locus_940_Allele_0 [BC_30_2.all]
---------------------------AA-------------TTCAGGTA----AA--------------------TTTT
TTA-----------G-A---A-----------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-------------------G----TGGTC---CCA---------------------------------------------
------------------AT-TCGTT---------------T--------------------------------------
--------------------------------------C-----------------------------------------
----------------------------------------AC-------A-ACAG-------------------------
------------------------------------------------AAATTA-----------ATCAA-----CCA--
----A--ATA---------------------------------------------TT-----------------------
------TT-T---------

RAxML code:

srun raxmlHPC-HYBRID-AVX -p 12345 -s alignment.fasta -n tree_test_6 -m GTRCAT -T $SLURM_CPUS_PER_TASK -N 4

[Alexandros Stamatakis]

On 11.06.2018 19:17, cav...@gmail.com wrote:
> I ran the following code for RAxML and instead of getting a tree for the
> populations or individuals it gave me a tree for each locus for each
> sample.

Well if you inferred a tree for each locus separately in a separate
alignment and not a concatenated one, that's pretty evident.

> I want know how to define the populations so that I can run a
> tree that shows how the populations are related.

You probably mean that you want to specify a constraint tree that would
constrain the ind. populations as monophyletic?

How this can be done is documented here:

https://sco.h-its.org/exelixis/resource/download/NewManual.pdf

and here:

https://sco.h-its.org/exelixis/web/software/raxml/hands_on.html

Alexis

>
>
> The alignment fasta file alignment.fasta look like this:
>
> >CLocus_2130_Sample_581_Locus_940_Allele_0 [BC_30_2.all]
> ---------------------------AA-------------TTCAGGTA----AA--------------------TTTT
> TTA-----------G-A---A-----------------------------------------------------------
> --------------------------------------------------------------------------------
> --------------------------------------------------------------------------------
> -------------------G----TGGTC---CCA---------------------------------------------
> ------------------AT-TCGTT---------------T--------------------------------------
> --------------------------------------C-----------------------------------------
> ----------------------------------------AC-------A-ACAG-------------------------
> ------------------------------------------------AAATTA-----------ATCAA-----CCA--
> ----A--ATA---------------------------------------------TT-----------------------
> ------TT-T---------
>
>
> RAxML code:
>
> srun raxmlHPC-HYBRID-AVX -p 12345 -s alignment.fasta -n tree_test_6 -m
> GTRCAT -T $SLURM_CPUS_PER_TASK -N 4
>

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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

[cav...@gmail.com]

I think maybe I did a poor job explaining it.  I have 20,000 loci and 128 individuals from 13 populations.  The problem is that I got a tree with 2,560,000 branches, or each loci times each individual.  I need the tree to have only 13 branches one for each population.  Do I do this using the partition method or is there an easier way.  I do not want to have to make a separate 2,560,000 text file, especially since the file does not seem to be in population order.

Thanks

[Alexandros Stamatakis]

I assume you want 13 subtrees, one for each population, correct?

A phylogenetic tree with 128 input sequences will necessarily have 253
branches. If you want each tree to have the same 13 subtrees containing
the populations you will need to specify a constraint tree via the -g
option.

Alexis

[cav...@gmail.com]

I am really very confused.  I want one tree with 13 branches one for each population.  The populations have various sample sizes from 3 to 17 for a total of 128 individuals.  I am not looking for a tree with just the branches for the individuals within a population as I do not believe that would be very informative.

Also what does the input file format look like for the -g option.  There are no examples given in the manual.

[Alexandros Stamatakis]

On 25.06.2018 22:34, cav...@gmail.com wrote:
> I am really very confused.  I want one tree with 13 branches one for
> each population.  The populations have various sample sizes from 3 to 17
> for a total of 128 individuals.  I am not looking for a tree with just
> the branches for the individuals within a population as I do not believe
> that would be very informative.

RAxML can not do that, it's a program for classic phylogenetic inference.

> Also what does the input file format look like for the -g option.  There
> are no examples given in the manual.

It's just a Newick tree file, see here for an example:

https://sco.h-its.org/exelixis/web/software/raxml/hands_on.html

Alexis

> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.

> > For more options, visit https://groups.google.com/d/optout

> <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
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>

[cav...@gmail.com]

So, from what you are telling me RAxML cannot do the classic tree where each node is a population, is this correct?

Is there any program that can do this analysis with such a large data set?

[Alexandros Stamatakis]

It does the classic tree inference just as any other program for
phylogenetic inference: given a set of input sequences it will infer a
tree containing all those input sequences as leaves ...

Alexis