I have one 560-bp long sequence for about 400 individuals. I understand that PhyML is faster, able to run with several model types, but non-partitioned, while RaxML can run with partitioned GTR models (not required here), the branch support is from bootstrapping only, but the result will be topologically more accurate.
That said, it’s still difficult to make a choice as I don’t know how much of topological details I will lose by running for 3 days shorter. Any advice would be very welcome.
Thank you!
Amael