This repository includes scripts and datasets for the paper, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge." All data files in this repository are for analyses using the logdet distance matrix computed on the concatenated alignment. Data files for analyses using the average gene-tree internode distance matrix can be downloaded from the Illinois Data Bank (https://doi.org/10.13012/B2IDB-1424746_V1). The latest version of NJMerge can be downloaded from Github (https://github.com/ekmolloy/njmerge).

***When downloading datasets, please note that the following errors.***

In tools.zip, the compare_trees.py and the compare_tree_lists.py scripts incorrectly refer to the normalized symmetric difference as the normalized Robinson-Foulds distance. Because the normalized symmetric difference and the normalized Robinson-Foulds distance are equal for binary trees, this does not impact the species tree error rates reported in the study. This can impact the gene tree error rates reported in the study (see data-gene-trees.csv in data.zip), as FastTree-2 returns trees with polytomies whenever 3 or more sequences in the input alignment are identical. Note that the symmetric difference rate is always greater than or equal to the Robinson-Foulds error rate, so the gene tree error rates reported in the study are more conservative.