Consensus tree building

Command: --consense [ STRICT | MR | MR<n> | MRE ]

Example: raxml-ng --consense MRE --tree alltrees.nw --prefix consMRE

This command will build a consensus of multiple trees (e.g., bootstrap replicate trees) using one of the following methods:

Command	Meaning
--consense STRICT	Strict consensus tree: includes only those branches/bipartitions which are present in all replicate trees. Strict consensus tree typically contains polythomies (multifurcations), unless all replicate trees are identical.
--consense MR	(default) Majority-rule consensus: includes branches/bipartitions which are present in majority (>50%) of replicate trees. MR consensus tree can be either multifurcating or bifurcating, depending on the dataset.
--consense MR<n>	Majority-rule consensus with a custom cut-off: includes branches/bipartitions which are present in >n% of replicate trees.
--consense MRE	Extended majority-rule consensus: MR tree extended by adding compatible branches with the highest support until a strictly bifurcating tree is obtained. Please note that MRE tree is built using a greedy heuristic (adding most supported branches first), which means that optimal solution is not guaranteed to be found. Hence, MRE trees obtained from the same tree set can differ, depending on the tool (e.g., RAxML-NG vs. RAxML) or even tree order in the input file. Typically, MRE tree is bifurcating, unless no "full" set of compatible branches can be found.