Non-standard genetic code

[lcscs...@gmail.com]

Hi,

Thank you for creating such a user friendly toolkit. One of the species in my analysis has non-standard genetic codes. Any suggestion?


Best,
Chun Shen

[françois SERRA]

Hi Chun,

for which function/tool of ete3 do you need the translation for?

thanks

francois

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François Serra

*Postdoctoral Fellow*

Structural Genomics Team - CNAG - Centre Nacional d’Anàlisi Genòmica
Structural Genomics Group - CRG - Centre de Regulació Genòmica
Parc Científic de Barcelona – Torre I
Baldiri Reixac, 4
08028 Barcelona
Tel: +34 934 020 828

[Jaime Huerta Cepas]

Hi Chun, 

where did you find a problem?

I don't see any potential issue in using non-genetic codes (as far as ete3 build workflows use external tools that support it).

  

On 16 March 2017 at 10:53, <lcscs...@gmail.com> wrote:

[lcscs...@gmail.com]

Hi,

I would like to do branch and branch-site LRT tests. I'm new to both etetoolkit and codeml. I've gone through paml manual and couldnt find a way to use codon table other than the standard one.

I also have a look at --codeml_help and it shows the default options in codeml.

[lcscs...@gmail.com]

Note that I'm using ete3 evol. The species that use non-standard genetic codes (translation table 12) is a Candida sp.

[l.fr...@gmail.com]

Dear all,
first of all thanks a lot for ete3. I like it a lot.

I am trying to run "ete3 evol" to investigate if natural selection is potentially acting on my sequences.
My sequences are mitochondrial genes of an insect (genetic code #5 on NCBI, invertebrate mitochondrial -- it corresponds to the genetic code #4 in codeml).

I ran the following command:

ete3 evol -t ouput_tree/clustalo_default-none-none-raxml_default/ATP6.fasta.final_tree.nw --alg ouput_tree/clustalo_default-none-none-raxml_default/ATP6.fasta.final_tree.used_alg.fa -o r7/ --models fb M2 --codeml_param icode,4 --cpu 3 --view


The GUI shows up correctly and the codeml results should be correct because I am providing the icode parameter to codeml.
However, the sequence alignment displayed in the GUI has not been translated with the correct genetic code. ete3 uses the universal code. Is it possible to tell ete3 to use another genetic code for the alignment?

Thanks a lot for your help.

Luca

[françois SERRA]

Hi Luca,

there is actually no way to tell ete3 to use an other genetic code, as you noticed the part involving CodeML is correct, but I haven't added other genetic codes yet. I will open an issue, to fix this point in a near future.

What you can do, is to change the source yourself in the translate function, here: https://github.com/etetoolkit/ete/blob/master/ete3/evol/utils.py#L119

and reinstall ete3.

for example, starting from the beginning:

git clone https://github.com/etetoolkit/ete/tree/master/ete3

cd ete3

cd ete3/evol
###

# edit the utils.py file, changing the genetic code
###

cd ../../

(sudo) python setup.py install

cheers,

francois

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[Julien Richard Albert]

Dear ete3 maintainers,

Thank you for ete3 - it's fantastic.

Sorry for bumping this old thread, but I too share the requirement of using a non-standard genetic code and I haven't found an available workaround since the last post here.

Has this been updated and I  just can't find it?

Cheers,

Julien

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[dengzi...@gmail.com]

Thanks for your reply! I will look into it

Best,

Ziqi