CONCAT species trees

The CONCAT trees were built using maximum likelihood (ML) based on the concatenated alignments of the 381 global marker genes (i.e., a “supermatrix”). The topology was inferred using RAxML under the LG + CAT model. The branch lengths were optimized using IQ-TREE under the LG + Gamma model. Branch supports are 100 rapid bootstraps (xboot).

• cons: Based on up to 100 most conserved sites per gene, as selected using the Trident algorithm.
• rand: Based on 100 sites randomly selected from sites with less than 50% gaps.
• Tree collapsed by xboot threshold = 50 are provided.

In addition, there is:

• fast: Based on all sites with less than 50% gaps, using the faster but less accurate ML implementation FastTree. Branch supports are 100 classical bootstraps (boot).

Also see:

• 1k: Downsampled to 1,000 taxa to allow using more complex models (PMSF) or more sites.

For comparative purpose, there is:

• rpls: Based on 30 ribosomal proteins instead of the 381 global markers. Because the total lengths of sequences are short, we used all sites with less than 50% gaps.