DOI: 10.5061/dryad.cs59t13
title: Data from: INSTRAL: discordance-aware phylogenetic placement using quartet scores

description: Phylogenomic analyses have increasingly adopted species tree
 reconstruction using methods that account for gene tree discordance using
 pipelines that require both human effort and computational resources. As
 the number of available genomes continues to increase, a new problem is
 facing researchers. Once more species become available, they have to
 repeat the whole process from the beginning because updating species trees
 is currently not possible. However, the de novo inference can be
 prohibitively costly in human effort or machine time. In this paper, we
 introduce INSTRAL, a method that extends ASTRAL to enable phylogenetic
 placement. INSTRAL is designed to place a new species on an existing
 species tree after sequences from the new species have already been added
 to gene trees; thus, INSTRAL is complementary to existing placement
 methods that update gene trees.
description: 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