Dear Alexis,
Good Morning!
I used raxmlHPC command for my alignment and it took me more than a month to align my 1.4 Mb genomic sequences of 779 isolates. So, I looked for a quicker way to generate raxml tree and I could see that raxmlHPC-PTHREADS-SSE3 is substantially faster. I submitted my alignment to the server with a total core of 16 cores and assigned 12 threads for my analysis. So, could you please kindly tell me how long it will take to get ML tree using this command? Will it be ready within a week?
raxmlHPC-PTHREADS-SSE3 -s Suberis_lcb_masked.fasta -m GTRGAMMA -f a -p 12345 -x 12345 -T 12 -N 1000 -n raxml_prasnp_concatenated_LCB_1055sites_masked_100boot.
Could you please let me know if there are any other alternatives to quickly prepare ML tree using raxml?
Thank you.
On Sep 8, 2022, at 8:37 AM, Alexandros Stamatakis <alexandros...@gmail.com> wrote:
The execution time can not be predicted as RAxML optimizes the tree iteratively and we never know how many iterations it will take.
What is helpful though is to first conduct just maybe one BS replicate search and then extrapolate from there.
It is also helpful to know the alignment dimensions in order to determine the approximate memory requirements and number of threads that can be used.
Please read the extensive RAxML documentation at https://urldefense.com/v3/__https://cme.h-its.org/exelixis/web/software/raxml/index.html__;!!Mih3wA!A_dcHp3tm0ET001XtAEsVFZAyv8NFax15STcwns2amBEL-Nj05YmVU3YO1doSGZBZ_6YRixpola-Do7XO0UR9_3ug5s$
and consider switching to RAxML-NG https://urldefense.com/v3/__https://github.com/amkozlov/raxml-ng__;!!Mih3wA!A_dcHp3tm0ET001XtAEsVFZAyv8NFax15STcwns2amBEL-Nj05YmVU3YO1doSGZBZ_6YRixpola-Do7XO0URrvBbx6w$ as standard RAxML is not being supported any more.
Alexis
On 08.09.22 11:34, krishna acharya wrote:
Dear Alexis,
Good Morning!
I used raxmlHPC command for my alignment and it took me more than a month to align my 1.4 Mb genomic sequences of 779 isolates. So, I looked for a quicker way to generate raxml tree and I could see that raxmlHPC-PTHREADS-SSE3 is substantially faster. I submitted my alignment to the server with a total core of 16 cores and assigned 12 threads for my analysis. So, could you please kindly tell me how long it will take to get ML tree using this command? Will it be ready within a week?
raxmlHPC-PTHREADS-SSE3 -s Suberis_lcb_masked.fasta -m GTRGAMMA -f a -p 12345 -x 12345 -T 12 -N 1000 -n raxml_prasnp_concatenated_LCB_1055sites_masked_100boot.
Could you please let me know if there are any other alternatives to quickly prepare ML tree using raxml?
Thank you.
Krishna
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Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas
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