Command Line Program For Constructing Phylogeny Tree In Minutes (500 Sequences)?

Question

[onpelikan]

Hi, can you help me please with choosing the command line program/tool which is able to construct phylogenetic tree from 500 sequences in few minutes on standard machine/notebook (better is only one core).

I tried: raxmlHPC-SSE3 and its 17min for 200 sequences. End for 400 sequences is in hours. I tried some others but with similar results. Is there something wrong or is there some program/tool that can do that faster?

Thank you very much.

Answer 1

[cts]

How about FastTree, it should easily handle 500 in a few minutes

[onpelikan]

Thank you very much. The FastTree is really fast. But some problem with the root occurs. Here is another question about it: FastTree - how to remove trifurcation inside tree?