Phylogenetic analysis for large size fasta sequences

Question

[MAPK]

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.

[lieven.sterck]

RaxML ? not sure on the multithreaded though

[GenoMax]

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

Edit: For step one. MSA.

[MAPK]

Aren't those designed for sequence alignment?

[GenoMax]

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.

[MAPK]

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

[Shri hari]

you can use https://github.com/stamatak/standard-RAxML it works fine for me

[sina.majidian]

Any new tools for this issue?

[Mehmet]

I recommend IQ-TREE2, which is very fast and you can use AUTO option that IQ-TREE automatically detects how many threats are needed and needs to be use.

Answer 1

[Shalu Jhanwar]

For phylogenetic analysis, MrBayes (http://nbisweden.github.io/MrBayes/) and FastTree (http://www.microbesonline.org/fasttree/#OpenMP) both supports multi-threading/parallelization.

Answer 2

[h.mon]

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.