Extra data for weighted ASTRID

s100_missing_data

Contains 50 replicates, each with 200 gene trees from the S100¹ dataset (seqlen = 400). The species tree is also provided in s_tree.trees to enable full reproduction of the results.

Fixed number of taxa deleted

The file names are in the form of g200.p{x}.tre, where $x$ is the amount of taxa randomly sampled and removed for each gene tree randomly. For example $x = 0.8$ means that 80% of the taxa each gene tree are sampled and removed. The support values and branch lengths are reevaluated by IQ-TREE using the following command using aBayes support:

iqtree2 -nt 1 -m GTR+G -abayes -t $tree -s $alignment_with_taxa_removed

Clade-based missing taxa

The file names are in the form of g200.clade.p{x}.tre, where $x$ is the lower bound of a candidate clade in the species tree. For example $x = 0.2$ means that only clades that are above 20% in size in the species tree are candidates.

Scripts

Scripts should be run from their respective directories as the working directory.

All scripts depend on TreeSwift. As such the scripts are licensed as GPL-3.0. Additionally, they depend on BioPython and.

s100_missing_data/count_leaves.py # count the number of leaves in each clade-based gene tree
random_clade.py # generate clade-based missing data for gene trees
random_missing.py # generate fixed-number-of-taxa-missing gene trees

Note

These data are provided for the purpose of reproducing the results. The ownership of the data belongs to the authors of the original paper.

Footnotes

1. Zhang, C., Rabiee, M., Sayyari, E., Mirarab, S.: ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19(6), 153 (2018). ↩