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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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two-steps reconstruction approach #104

Closed fujch7 closed 3 years ago

fujch7 commented 3 years ago

Hi developers,

Is this a two-step tree building method like raxml? by deriving the first phylogeny with any of the available approaches and then refine it in a second step using RAxML.

Many thanks!

amkozlov commented 3 years ago

Well you can specify your first-step phylogeny as a starting tree via --tree option. In some cases, it can decrease tree inference time, but also increase the risk of hitting a local optimum. In general, there is no guarantee that a "better" starting tree leads to a better-scoring final ML tree. We therefore recommend using multiple distinct starting, which is now the default in RAxML-NG.

amkozlov commented 3 years ago

closing since the question was answered