Question: Phylogenetic analysis for large size fasta sequences
0
gravatar for MAPK
24 months ago by
MAPK1.5k
Washington University in St. Louis
MAPK1.5k wrote:

I am trying to run phylogenetic analysis for maximum likelihood tree. I have a large dataset (fasta sequences) which is just impossible to run in Mega. Is there a better option that I can resort to so I could use as many computing resources as I want. I need to use a minimum of 500gb ram to do this analysis and I was thinking to do this in HPC cluster. Any suggestion on the tool with multi-threading option would be really appreciated.

phylogenetics • 1.2k views
ADD COMMENTlink modified 24 months ago by h.mon29k • written 24 months ago by MAPK1.5k
1

RaxML ? not sure on the multithreaded though

ADD REPLYlink written 24 months ago by lieven.sterck7.8k

Muscle, MAFTT, T-Coffee should all be good alternatives assuming you have access to necessary hardware.

Edit: For step one. MSA.

ADD REPLYlink modified 24 months ago • written 24 months ago by genomax83k

Aren't those designed for sequence alignment?

ADD REPLYlink written 24 months ago by MAPK1.5k

Creating alignments for very large sequence datasets can be computationally very challenging and that is where MEGA could be struggling. Take a look at this publication to have a new perspective on this topic.

ADD REPLYlink written 24 months ago by genomax83k

Alignment was rather easy. Mega was struggling with model testing steps and bootstrapping during maximum likelihood analysis.

ADD REPLYlink written 24 months ago by MAPK1.5k
0
gravatar for h.mon
24 months ago by
h.mon29k
Brazil
h.mon29k wrote:

ExaML, RAxML-NG or RAxML (from faster to slower). All three are from the same group, and all three support MPI parallelization, making them suitable to HPC clusters.

ADD COMMENTlink modified 24 months ago • written 24 months ago by h.mon29k
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