Hey all, I'm new to using MAFFT. I've got it working on my machine using a docker image, and can get output from it. I have also used the online version here https://mafft.cbrc.jp/alignment/server/
What it is attempting to do is obviously a hugely computationally expensive process. Aside from choosing different algorithms, or renting time on a powerful HPC VM, are there ways to increase the speed that MAFFT works at?
Some other things I am wondering:
- When running it, I can set --thread 8 --threadtb 5 --threadit 0. However, when I use the command htop to check my core usage, only 2 or 3 cores are ever being used. Is there a way to force more parallelism? While I am using Docker to run it, I am running Docker using --cpuset-cpus="0-6", which should allow the program to access up to 7 cores. CPU use never gets above 40%.
- Is there a GPU enhanced version readily available, to get more performance?
- Is there any "trick-of-the-trade" that I am maybe unaware of right now, that can be used to squeeze a bit more performance from it?
Sticking to Docker images would be my preferred method - however, if there are builds of mafft out there that are Docker-ised yet but are faster, I'd be interested in using them.