Underlying trees in the GeneTrees

Starting from this release (65), we provide further details on the internal aspects of the GeneTrees. Our trees are built using a several phylogenetic reconstruction methods, each of them resulting in a different tree. These are combined by TreeBeST to produce final tree (Read more on the pipeline). Each node of the final tree is supported by at least one of the original trees.

The new functionality is not quite like an X-ray plate, but you can click on any node to find out about which methods support this particular node. The 5 methods we use for protein-coding gene trees are:

  • phyml_aa: maximum likelihood (ML) tree based on the protein alignment with the WAG model
  • phyml_nt: ML tree based on the codon alignment with the HKY model
  • nj_mm: neighbour-joining (NJ) tree based on the codon alignment using p-distance
  • nj_dn: NJ tree based on the codon alignment using dN distance
  • nj_dn: NJ tree based on the codon alignment using dS distance

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