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Ancestral state reconstruction

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Alexey Kozlov edited this page Nov 20, 2019 · 3 revisions

Command: --ancestral

Example: raxml-ng --ancestral --msa ali.fa --tree best.tre --model HKY --prefix ASR

RAxML-NG implements marginal ancestral state reconstruction using the 'classical' empirical Bayesian method (same method is supported by PhyML and IQTree).

NOTE: RAxML8.x implemented a different approach to ancestral state reconstruction (-f A option), thus its results cannot be directly compared to RAxML-NG.

NOTE: By default, RAxML-NG will re-use existing labels as inner node identifiers. If this is not desired (eg. your tree is annotated with bootstrap support values), please make sure you remove those node labels before calling the --ancestral command. Then, RAxML-NG will assign new unique node labels (NodeX).

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