The phrase "a super tree" is correct and usable in written English.
It can be used in contexts discussing a type of tree that has enhanced characteristics or abilities, often in a scientific or fictional context.
Example: "The researchers discovered a super tree that could absorb twice as much carbon dioxide as regular trees."
Alternatives: "an enhanced tree" or "a superior tree".
We used Purvis' [ 65] estimate of primate phylogeny, which was created using a super-tree technique to combine a large number of source phylogenies.
Using the weighted MRP method [ 24], we combined these trees to reconstruct a super-tree that would reflect a consensual scenario of T6SS evolution.
A second tree was reconstructed using a super-tree approach as implemented in Duptree [ 71], this algorithm tries to find the species tree that minimizes the number of duplication events that occurred in a set of gene trees.
Finally, we combined all individual gene trees into a super-tree by finding the species tree that implies the least number of total duplications in single-gene trees [ 31].
In addition, a super-tree was reconstructed from the 4,965 gene phylogenies contained in the N. delphensis phylome, using a tree parsimony approach as implemented in DupTree [ 20].
The Streptococcus study used BlastClust [ 41] for homology inference, t-coffee [ 42] for protein alignment, a super-tree from 1-1 orthologs using BIONJ [ 43] and implemented filters to remove sequences smaller than 100 nucleotides, sequences with frameshift mutations or groups with evidence of recombination.
The E. coli study used an in-house algorithm for homology inference, ClustalW for protein alignment, a super-tree computed using all groups evaluated and implemented filters to remove sequences with low mean similarity, sequences with frameshift mutations, sequences with paralogs and groups with evidence of recombination.
Rather, the conclusion is that when seeking solutions to a new wave of phylogenetic problems (super tree algorithms, gene vs. species tree, mixture models), invariant based methods should be considered.
