Data from: INSTRAL: discordance-aware phylogenetic placement using quartet scores

EPA-ng results for concatenationThe EPA-ng output files for concatenation tree and concatenated alignmentsconcatenation-epa.tar.gzTrue Species TreesThe true species trees for all model conditions simulated using SimPhytrue-specis-trees.tar.bzEstimated gene treesEstimated gene trees for the three model conditions with speciation rate of 0.000001. There are three folders corresponding to the three ILS level and in each folder there are 50 replicates each containing 1000 gene trees in newick format.estimatedgenetrees.0.000001.tar.gzEstimated gene treesEstimated gene trees for the three model conditions with speciation rate of 0.000001. There are three folders corresponding to the three ILS level and in each folder there are 50 replicates each containing 1000 gene trees in newick format. The name 'model.200.500000.0.0000001' means the number of species is 200, number of generations is 500000 and speciation rate is 0.0000001.estimatedgenetrees.0.0000001.tar.gzgene trees for 10K datasetEstimated gene trees for the very large dataset, used for running time analysis10k.genetrees.1.tar.gzgene trees for 10K datasetEstimated gene trees (part 2 ) for the very large dataset, used for running time analysis10k.genetrees.2.tar.gzBiological datasetsThe estimated gene trees and species trees for the three biological datasets are included. The intermediate and final trees for ordered placement are also included in 'hierarchical-placement'.biological-datasets.tar.gzBackbone trees for ordered placementBackbone trees used for ordered placement for simulated dataset with 201 species trees, which are estimated species trees created from 50, 200 and 1000 gene trees. 50, 100 and 150 leaves are pruned which are specified by 'x.pruned' in the names.ordered-placement-backbones.tar.gzEPA-ng gene trees (low ILS)Estimated gene trees for simulated dataset with low ILS. For each set of gene trees (200 genes), one species has been pruned and then placed back using EPA-ng. The number in folder name, e.g. sp100 is the label of species being pruned and then placed back.epa_genetrees.model.200.10000000.0.000001.tar.gzEPA-ng gene trees (medium ILS)Estimated gene trees for simulated dataset with medium ILS. For each set of gene trees (200 genes), one species has been pruned and then placed back using EPA-ng. The number in folder name, e.g. sp100 is the label of species being pruned and then placed back.epa_genetrees.model.200.2000000.0.000001.tar.gzEPA-ng gene trees (high ILS)Estimated gene trees for simulated dataset with high ILS. For each set of gene trees (200 genes), one species has been pruned and then placed back using EPA-ng. The number in folder name, e.g. sp100 is the label of species being pruned and then placed back.epa_genetrees.model.200.500000.0.000001.tar.gzSupplementary-material