alignments

All files are tar.bz; thus, you should decompress using tar xvfj [file name].

Gene alignments

We include the final single-copy alignment files used for gene tree and species tree analyses.

The following are the alignments after all main filtering steps have been applied.

1. alignments-FAA-masked.tar.bz: These are the alignments used in the main results, including Figure 2.
2. alignments-C12-masked.tar.bz

These are alignments after the initial filtering steps but before filtering gappy sits and fragmentary sequences

1. alignments-FAA.tar.bz: The FAA alignments, one file per gene.
2. alignments-C12.tar.bz: The FNA2AA alignments, with C3 removed, one file per gene. The .part files show the boundary between C1 and C2. Note that C1 positions come before C2 positions.
3. alignments-FNA2AA.tar.bz: The FNA2AA alignments, with all three codon positions, one file per gene.

And here is the FAA alignment before even filtering of insertion sites in UPP.

1. alignments-FAA-unmasked.tar.bz: The unmasked FAA alignment, one file per gene

Supermatrix alignments

1. concat/FAA-upp-masked.fasta.mask10sites.mask33taxa.tar.bz Concat supermatrix of unfiltered FAA alignment of gene trees.
2. concat/FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.tar.bz Concat supermatrix of unfiltered FNA2AA alignment of gene trees.
3. concat/filtered_FAA-upp-masked.fasta.mask10sites.mask33taxa.tar.bz Concat supermatrix of FAA alignment of gene trees after removing rouge taxa
4. concat/filtered_FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.tar.bz Concat supermatrix of FNA2AA alignment of gene trees after removing rouge taxa
5. concat/tree_FAA-upp-masked.fasta.mask10sites.mask33taxa.tar.bz Concat supermatrix of FAA alignment of gene trees of only the eudicot species.
6. concat/tree_FNA2AA-upp-masked-c12.fasta.mask10sites.mask33taxa.tar.bz Concat supermatrix of FNA2AA alignment of gene trees of only the eudicot species.