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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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Comprehensive tree as a toplogical constraint #81

Closed pyspider closed 4 years ago

pyspider commented 4 years ago

Hi， I am trying to infer a phylogenetic tree from a trimmed alignment. And I want to use a previous tree as a topological constraint (--tree-constraint/-g) that was generated from full matrix. I encountered this error when I used a comprehensive tree as a topological constraint on raxml-ng. ERROR: You provided a comprehensive, fully-resolved tree as a topological constraint. Since this is almost certainly not what you intended, RAxML-NG will now exit... However, It seems that raxml can work using same constraint tree. raxmlHPC-HYBRID -T 4 -n mitochondrial_result -s infile.txt -m GTRGAMMA -p 12345 -g constraint.tre -f a -N 1000 -x 12345 --asc-corr lewis I am not sure whether raxml-ng doesn't allow to use a comprehensive tree. But raxml can use this constraint tree. Does I can use a comprehensive tree from full matrix as a topological constraint tree to infer a new phylogenetic tree using a reduced subset of full matrix on raxml/raxml-ng?

amkozlov commented 4 years ago

Well if your constraint tree is comprehensive (=contains all taxa) and fully-resolved (=binary), there is no sense to perform tree search since there is one single topology which satisfies the constraint (=constraint tree itself). That's why RAxML-NG exits with error.

If your goal is to optimize branch lengths and model parameters on the trimmed alignment, please use --evaluate command instead.

amkozlov commented 4 years ago

I consider this one solved -> closing.