limited number of genomes

[t k]

Hi,

Could you please tell me how to increase the number of fasta/contig genomes for phame analysis? (ten genomes could be added only).

best,

Tomasz

[micro...@gmail.com]

Hi Tomasz, you can try the stand-alone version of PhaME, which doesn't have any limits on the number of genomes. However, that is a command-line tool. Here is its repo that also contains information on how to install it.

https://github.com/LANL-Bioinformatics/PhaME

Thank you and let me know if this works for you.

- migun

[Lo, Chien-Chi]

On the public server, we have limit the number.

 

If you have local instance EDGE or you have access to the system, you can edit the edge configuration file.

 

EDGE system configuration file is $EDGE_HOME/edge_ui/sys.proprties. You can edit this file to turn on/off EDGE functions/modules (on=1, off=0) or adjust some module parameters;

For example ## modules parameters

edge_ref_genome_file_max=20

edge_phylo_genome_file_max=20:

 

Thanks,

Chienchi

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[t k]

Thank you for your prompt response. 

I have read that Phame can identify signs of positive, negative and neutral selection among genomes:

"Identifying SNPs found in coding regions enables further molecular evolutionary analyses -a post-phylogeny option that is provided in PhaME. PhaME uses the HyPhy package Branch-Site random effects likelihood (REL) model for detecting episodic diversifying selection on all genes containing at least 1 SNP, as well as on a concatenation of all these genes." (https://www.biorxiv.org/content/10.1101/032250v1.full)  

Is this possible through Edge or I should install a stand-alone version of Phame to identify selection?

best wishes,

Tomasz

To view this discussion on the web visit https://groups.google.com/d/msgid/edge-users/46577B65-E068-4AF9-9AF6-99E01214C762%40lanl.gov.

--

Dr. hab. Tomasz Kulik, Department of Botany & Nature Protection, University of Warmia & Mazury in Olsztyn, Plac Lodzki 1, Olsztyn 10-957, Poland, Phone +48895234511

[t k]

Hi,

Editing the edge configuration file does not work. Still only 10 genomes can be analyzed on local instance edge.

t

[Lo, Chien-Chi]

Sorry! Editing the configuration will allow more genomes been processed by the back-end command lines tools which means you can select more genomes from the Select Genome(s) (drop down search).   The GUI has hard-coded limit “Add Genomes(s)” to 10 for user genomes.

 

Thanks,

Chienchi

To view this discussion on the web visit https://groups.google.com/d/msgid/edge-users/d02e4b0f-8682-404f-8ebd-98277d560b75n%40googlegroups.com.