ASTRAL tree

The tree was built using the gene tree summary tool: ASTRAL.

Go to GitHub directory.

Branch supports

The internal branch of an ASTRAL tree typically receive three support statistics:

  1. EN (effective number of genes): number of gene trees that contain some quartets around that branch.
  2. QT (quartet score) (Sayyari and Mirarab, 2016): Proportion of the quartets in the gene trees that support this branch.
  3. LPP (local posterior probability): the probability this branch is the true branch given the set of gene trees (computed based on the quartet score and assuming ILS).

We recommend using LPP as a general measure of the confidence of a branch. Note that this metric should not be confused with the posterior probability calculated using the Bayesian method.

We also provide trees in which branches with EN <= 5 or LPP <= 0.5 (abbr.: e5p50) are collapsed. We recommend using the collapsed tree, which has higher confidence in the accuracy of topology, for downstream applications.

Branch lengths

In an original ASTRAL tree, the branch lengths are in coalescence units. The trees under the branch_length directory have the same topology (and node IDs) to the original tree, but with branch lengths re-estimated using ML, based on three concatenated alignments:

  • cons: Up to 100 most conserved sites per gene, as selected using the Trident algorithm.
  • rand: 100 sites randomly selected from sites with less than 50% gaps.
  • rpls: 30 ribosomal proteins instead of the 381 global markers. We do not recommend using this tree as a reference.

The resulting branch lengths represent the expected number of amino acid substitutions per site, which is the conventional metric used in most phylogenetic trees, including the CONCAT trees.

We also provide ultrametric trees (i.e., all tips have equal distance to root), which may be useful in some applications. They were generated using r8s.