Re: phylogenetic tree construction time

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Anitha Bavikatte

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Jul 29, 2021, 12:16:43 AMJul 29
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Hello everyone,

I created phylip format from vcf (vcf2phylip) has 85 samples (Alignment sites/patterns: 88863527 / 81088710), started raxml-ng by using
 "/raxml-ng --bootstrap --msa phylogeny.min4.phy --model GTR --bs-trees 200 --threads 10 -outgroup"
command, how much time it will take to create the final best model if any parameters need to add to improve the efficiency of the tool. my system configuration is 16 cores, 503 GB RAM.

Thanks and regards,
Anitha B N

Alexey Kozlov

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Jul 29, 2021, 7:11:32 PMJul 29
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Hi Anitha,

first, this command will generate bootstrap trees only, but not the ML, please read raxml-ng
documentation and tutorial:

https://github.com/amkozlov/raxml-ng/wiki/Tutorial

Second, your dataset is really large, please either try to reduce it, or you would probably need a
larger servers / multiple cluster nodes to analyze it in reasonable time.

Hope this helps,
Alexey

On 29.07.21 06:16, Anitha Bavikatte wrote:
> Hello everyone,
>
> I created phylip format from vcf (vcf2phylip) has 85 samples (Alignment sites/patterns: 88863527 /
> 81088710), started raxml-ng by using
> * "/raxml-ng --bootstrap --msa phylogeny.min4.phy --model GTR --bs-trees 200 --threads 10 -outgroup"*
> command, how much time it will take to create the final best model if any parameters need to add to
> improve the efficiency of the tool. my system configuration is 16 cores, 503 GB RAM.
>
> Thanks and regards,
> Anitha B N
>
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Anitha Bavikatte

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Jul 29, 2021, 10:40:56 PMJul 29
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Thanks for reply. Raxml already created model that's why I started using bootstrap. This option is there in tutorial.

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