Weighted-ASTRAL_data

S200 dataset

File organization

Folder structure: S200/model.200.${TREE_HEIGHT}.${BIRTH_RATE}/${REPLICATE_NUMBER}/${TREE_FILE}

For estimated gene trees: TREE_FILE=estimatedgenetre for SH-like support and TREE_FILE=estimatedgenetre.abayes for approximate Baysian support

For estimated species trees: TREE_FILE=${INPUT_GENE_TREE}.${NUM_GENES_USED}.${RECORSTRUCTION_METHOD}, where RECORSTRUCTION_METHOD=astral-weighted for support-weighted version (wASTRAL-s) and RECORSTRUCTION_METHOD=astral-hybrid for hybrid-weighted version (wASTRAL-h)

For true species trees: TREE_FILE=s_tree.trees

Large Data Files

The original dataset can be found here, and sequence data can be found here.

Missing Taxa

The gene trees with simulated missing taxa (Figure 4) and estimated species trees can be accessed here.

S100 dataset

File organization

True species trees are located at S100/${REPLICATE_NUMBER}/s_tree.trees.

Folder structure for estiamated trees: S100/${REPLICATE_NUMBER}/bestMLestimatedgenetree/${TREE_FILE}

For estimated gene trees: TREE_FILE=estimatedgenetre_${GENE_LENGTH}.gtr.rerooted.final.contracted.non for Bootstrap support and TREE_FILE=estimatedgenetre_${GENE_LENGTH}.gtr.rerooted.final.contracted.non.abayes for approximate Baysian support.

For estimated species trees: TREE_FILE=${INPUT_GENE_TREE}.${NUM_GENES_USED}.${RECORSTRUCTION_METHOD}, where RECORSTRUCTION_METHOD=astral-weighted for support-weighted version (wASTRAL-s) and RECORSTRUCTION_METHOD=astral-hybrid for hybrid-weighted version (wASTRAL-h).

Large Data Files

The original dataset including estimated gene trees, true species trees, ASTRAL estimated species trees, and sequence data can be found here.

We also keep estimated gene trees with Bootstrap support, true species trees, and new estimated gene trees with approximate Baysian support here.

Biological datasets

File organization

Estimated gene trees are located at biological/gene_trees/${DATASET}_${WEIGHTING_METHOD} (expect for Canis which is too large), where WEIGHTING_METHOD=bs for Bootstrap, WEIGHTING_METHOD=sh for SH-like, and WEIGHTING_METHOD=bayes for approxiamte Bayesian.

Estimated species trees are located at biological/species_trees/${DATASET}_${RECORSTRUCTION_METHOD}${_OPTIONAL_WEIGHTING_METHOD}, where RECORSTRUCTION_METHOD=hybrid for weighted ASTRAL with hybrid weighting, RECORSTRUCTION_METHOD=astral for ASTRAL-III, RECORSTRUCTION_METHOD=concat for concatenation, RECORSTRUCTION_METHOD=published for the approach published in the source paper.

One thousand plant (1kp)

One thousand plant transcriptomes and the phylogenomics of green plants

All data can be found here.

Canis dataset (dog)

Interspecific Gene Flow Shaped the Evolution of the Genus Canis

Original Sequence data can be found here. We also keep estimated gene trees here.

Avian (avian14k)

Whole-genome analyses resolve early branches in the tree of life of modern birds

We keep estimated gene trees here.

Cetacean (whale)

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

All data can be found here.

Insect-Pseudapis (bee)

Gene Tree Estimation Error with Ultraconserved Elements: An Empirical Study on Pseudapis Bees All data can be found here

Insect-Lepidoptera (butterfly)

Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths

All data including gene trees can be found here.

Insect-Papilionidae (swallowtail)

Whole Genome Shotgun Phylogenomics Resolves the Pattern and Timing of Swallowtail Butterfly Evolution

All data can be found here.