Core phylogenetic tree/CIPRES

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chiara Sgaramella

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Mar 21, 2024, 10:52:39 AMMar 21
to raxml
Hi everyone,
I have to produce a core phylogenetic tree.I have 250 genomes and i have aligned them through roary and created a core_gene_alignment file.
I have a MacBook Air 2020.Yesterday i tried to run this two commands but my computer crushed. 
 1)raxml-ng --parse --msa [file.aln] --msa-format FASTA --model GTR+G --prefix T1
2)raxml-ng --all --msa T1.raxml.reduced.phy --model GTR+G --prefix T2 --seed 2 --tree pars{50},rand{50} --bs-trees 1000 --bs-metric fbp,tbe

1)If i want to conduct the same type of analysis using CYPRES Science Gateway which of the: RAxML-HPC BlackBoxRAxML-HPC2 on ACCESSRAxML-HPC2 Workflow on XSEDERAxML-HPC v.8 on ACCESSRAxML-NG on ACCESS i have to use and with which parameter.

2) If I need to use another computer: which type of processor will be suitable for this type of analysis?

Thank you in advance 

Pfeiffer, Wayne

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Mar 22, 2024, 1:50:07 AMMar 22
to ra...@googlegroups.com, Pfeiffer, Wayne
Please use RAxML-NG on ACCESS to run RAxML-NG via CIPRES.

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