weighted ASTRAL:

Zhang, C., & Mirarab, S. (2022). Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees. Molecular Biology and Evolution, 39(12), msac215. https://doi.org/10.1093/molbev/msac215.

• Refer to this page all the data: https://github.com/chaoszhang/Weighted-ASTRAL_data 

ASTRAL-Pro:

Zhang, C., Scornavacca, C., Molloy, E. K., & Mirarab, S. (2020). ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy. Molecular Biology and Evolution, 37(11), 3292–3307. https://doi.org/10.1093/molbev/msaa139 

• Please refer to this GitHub: https://github.com/chaoszhang/A-pro_data/

Zhang, C., & Mirarab, S. (2022). ASTRAL-Pro 2: Ultrafast species tree reconstruction from multi-copy gene family trees. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac620 

• Please refer to this GitHub: https://github.com/chaoszhang/A-Pro2_data 

ASTRAL-MP:

Yin, J., Zhang, C., & Mirarab, S. (2019). ASTRAL-MP: Scaling ASTRAL to very large datasets using randomization and parallelization. Bioinformatics, 35(20). https://doi.org/10.1093/bioinformatics/btz211.

We have used the following datasets

• SV 10-1000 : These gene trees can be found on the ASTRAL-II subsection below.  

• Avian: This is the dataset with 48 species and 14446 gene trees with varying contractions. The gene trees, the  species trees generated by ASTRAL as well as the ASTRAL output can be found here https://datadryad.org/stash/dataset/doi:10.6076/D16W2H 

• Insects: This is the dataset with 144 species and 149278 gene trees. The gene trees can be found at https://doi.org/10.6076/D14599 

• Simulated 10K: This is the dataset with 10K species and simulated using SimPhy (20 replicates). 

• All the data can be found here: https://datadryad.org/stash/dataset/doi:10.6076/D16W2H 

• Scripts to generate the data and to analyze it are also found here: https://github.com/smirarab/astralmp-simulations 

ASTRAL-Multiind:

Rabiee, Maryam, Erfan Sayyari, and Siavash Mirarab. “Multi-Allele Species Reconstruction Using ASTRAL.” Molecular Phylogenetics and Evolution 130 (2019): 286–96. https://doi.org/10.1016/j.ympev.2018.10.033. 

• Refer to this gitlab for all the data: https://gitlab.com/mrabiee/ASTRAL-multiind/

INSTRAL:

Rabiee, Maryam, and Siavash Mirarab. “INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores.” Systematic Biology, July 10, 2019. https://doi.org/10.1093/sysbio/syz045.

• Data are available on Dryad: https://doi.org/10.5061/dryad.cs59t13

Polytomy test:

Sayyari, E., & Mirarab, S. (2018). Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies. Genes, 9(3), 132. https://doi.org/10.3390/genes9030132 

• • https://github.com/esayyari/polytomytest

  • https://gitlab.com/esayyari/polytomy  

ASTRAL-III:

Zhang, Chao, Maryam Rabiee, Erfan Sayyari, and Siavash Mirarab. “ASTRAL-III: Polynomial Time Species Tree Reconstruction from Partially Resolved Gene Trees.” BMC Bioinformatics 19, no. S6 (2018): 153. https://doi.org/10.1186/s12859-018-2129-y.

• For data, please refer to  https://gitlab.com/esayyari/ASTRALIII 

LocalPP:

Sayyari, E., & Mirarab, S. (2016). Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies. Molecular Biology and Evolution, 33(7), 1654–1668. https://doi.org/10.1093/molbev/msw079 

• • https://esayyari.github.io/FastLocalBranchSupport.html

ASTRAL-HGT study::

Davidson, Ruth; Vachaspati, Pranjal; Mirarab, Siavash; Warnow, Tandy (2023): Data from: Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. 

• • https://databank.illinois.edu/datasets/IDB-6670066

ASTRAL-II:

 Mirarab, S., & Warnow, T. (2015). ASTRAL-II: Coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics, 31(12), i44–i52. https://doi.org/10.1093/bioinformatics/btv234 

• Download simulation scripts from Github: https://github.com/smirarab/astral2sims 

• All the simulation and real data files are given in the Dryad:  https://doi.org/doi:10.6076/D10C7C. 

  • A full README.md on Dryad explains the content of the data files on Dryad