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They now agree with the tree's defenders.
However, the overall topology of both the cytochrome b tree and the nuclear tree largely agree with the tree obtained from the combined dataset of all genes.
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Tree topologies of the individual genes agreed with the tree constructed from the sequence concatenation (data not shown).
Surprisingly, no form of model produces trees that agree with the species tree provided by Ensembl.
This implies that the gene tree topology appearing most often when considering different genes might not agree with the species tree topology, thus we cannot use a simple majority-heuristic to infer the species tree from a collection of gene trees.
Overall, module enrichment/depletion did not agree with the evolutionary tree of the represented plants, in line with the seemingly heterogeneous birth/death rates of the entire FBX gene superfamily.
The NR3 subfamily only showed one difference because the NJ tree did not agree with the other trees as to the placement of the androgen receptor.
These results generally agree with the phylogenetic trees, indicating orthology between appropriate isoenzymes of human and fishes.
The application of noisy with cutoff qcutoff = 0.8, on the other hand, leads to consistent results for all methods including MP (Maximum Parsimony) that agree with the best trees reported in [ 25].
Contact: [email protected] The phylogeny of a gene family evolving by vertical descent will agree with the associated species tree.
We agree with the reviewer that the trees generally have a weakly supported backbone and that the CAD and CCR trees are likely affected by some degree of ancestral paralogy.
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