DOI: 10.5061/dryad.wstqjq2tk
title: Data from: Fast coalescent-based computation of local branch support from quartet frequencies

description: Species tree reconstruction is complicated by effects of incomplete
 lineage sorting, commonly modeled by the multi-species coalescent model
 (MSC). While there has been substantial progress in developing methods
 that estimate a species tree given a collection of gene trees, less
 attention has been paid to fast and accurate methods of quantifying
 support. In this article, we propose a fast algorithm to compute
 quartet-based support for each branch of a given species tree with regard
 to a given set of gene trees. We then show how the quartet support can be
 used in the context of the MSC to compute (1) the local posterior
 probability (PP) that the branch is in the species tree and (2) the length
 of the branch in coalescent units. We evaluate the precision and recall of
 the local PP on a wide set of simulated and biological datasets, and show
 that it has very high precision and improved recall compared with
 multi-locus bootstrapping. The estimated branch lengths are highly
 accurate when gene tree estimation error is low, but are underestimated
 when gene tree estimation error increases. Computation of both the branch
 length and local PP is implemented as new features in ASTRAL.
description: ## Simulations There are two simulated datasets that we used in this
 paper. ### ASTRALII dataset. This dataset contains estimated gene trees,
 true gene trees, true species trees, and inferred species trees with
 ASTRAL, RAxML, and NJST. Each archive contains a directory structure
 corresponding to: * model conditions (e.g.,
 `model.200.10000000.0.0000001`), and under each of them, it includes one
 folder per replicate `[rep]`. * `k` is either 1000, 200, or 50, and is the
 number of genes. * `method` is either `astral`, `njst`, `concat` and
 refers to the method used for inferring the species tree. * Two types of
 gene trees `[gt]` are used: true gene trees `true` and estimated gene
 trees `half`. Note that `_[gt]` is not specified for `concat` method
 because it is irrelevant. ##### Files: * `ASTRALII-BL.tar.gz`: The branch
 length estimations. *
 `model.200.10000000.0.0000001/01/astral-bl-[k]-[gt].txt`: A file where
 each row is an internal branch and branch lengths are given in coalescent
 units (first column) and in the unit of the number of generations (third
 column). * `model[model]/[rep]/astral/astral_[k]_[gt]_sp.nwk`: The tree
 with branch lengths in coalescent unit for internal nodes. Ignore terminal
 branch lengths, which are in generation time. *
 `model[model]/[rep]/astral/astral_[k]_[gt]_sp_Stat`: The log file of
 astral * ` ASTRALII-pp.tar.gz`: The posterior probability estimate files.
 Files are the species trees with posterior probability annotated (newick
 format). Files are of type: *
 `model.[model]/[rep]/astral/[method]_[k]_[gt]`: full astral annotation
 (like `-t 12`). * Note: poorly named
 `model.[model]/[rep]/astral/[method]_[k]_[gt]_sp` files correspond to true
 species trees scored. *
 `model.[model]/[rep]/astral/[method]_[k]_[gt]Stat`: ASTARL log files *
 `ASTRALII.tar.gz`: raw simulated datasets. Files are of type
 `data/ASTRALII/200-taxa/model.[model]/[rep]/*` and include: * True
 (simulated) species trees (`s_tree.trees`) * True (simulated) gene trees
 (`truegenetrees`) * Estimated gene trees (FastTree), removing those with
 low resolution (`estimatedgenetre.halfresolved`) * Inferred species trees
 with ASTRAL (`astral-v474-p1`), RAxML (`concatenatedtree`), and NJST
 (`njst`) from 50, 200, or 1000 genes (the 50 and 200 are the first from
 the `estimatedgenetre.halfresolved` or `truegenetrees` files). ### Avian
 simulated dataset. This dataset contains drectories of the form
 `noscale.1000g.[bp]/R[rep]/` where `[bp]` is the sequence length (250,
 500, 1000, 1500). In each directory, we have * `avian-astral.tre.blen`:
 Output of astral applied to bestML gene trees with correct branch lengths
 * `avian-astral.tre.blen.err`: ASTRAL log file when computing BL, applied
 to bestML input tree * `astral-bl.nwk`: ASTRAL tree with full annotations.
 * `genetrees.gt`: 1000 bestML gene trees * `astral/BS.[bsrep].tre`: MLBS
 ASTRAL results, bootstrap replicate numbered `[bsrep]`. 200 replicates are
 done. * `astral/Best.tre`: ASTRAL applied on bestML gene trees with no
 branch lengths * `astral/RAxML_bipartitionsBranchLabels.bestML`: greedy
 consensus of MLBS replicates, as done by RAxML. *
 `astral/avian-astral-truegene.nwk`: results of applying ASTRAL on true
 gene trees for the species tree inferred from gene trees of this
 directory. * `astral/avian-astral-truegene.nwk.info-estimatedgenetree`:
 ASTRAL log file of applying ASTRAL on true gene trees for the species tree
 inferred from gene trees of this directory. ## Biological datasets In this
 paper, we analyzed 4 different biological datasets. The results and the
 datasets are available at `Biological.tar.gz`: * Avian biological dataset
 of Jarvis et. al. available at paper: Jarvis, Erich D., et. al.
 "Phylogenomic analyses data of the avian phylogenomics project."
 GigaScience 4.1 (2015): 1-9. * These data are available at
 [http://dx.doi.org/10.5524/101041](http://dx.doi.org/10.5524/101041) * The
 dataset analyzed by Xi et. al. available at paper: Xi, Zhenxiang, Liang
 Liu, Joshua S Rest, and Charles C. Davis. “Coalescent versus Concatenation
 Methods and the Placement of Amborella as Sister to Water Lilies.”
 Systematic Biology 63, no. 6 (November 1, 2014): 919–932.
 [http://doi.org/10.1093/sysbio/syu055](http://doi.org/10.1093/sysbio/syu055). * See Dryad repo doi:10.5061/dryad.qb251 for sequences. Gene trees provided to us by authors. * The 1KP dataset analyzed by Naim Matasci et. al. published at: Matasci, N., Hung, L.H., Yan, Z., Carpenter, E.J., Wickett, N.J., Mirarab, S., Nguyen, N., Warnow, T., Ayyampalayam, S., Barker, M. and Burleigh, J.G., 2014. Data access for the 1,000 Plants (1KP) project. GigaScience, 3(1), pp.1-10. * Data available on iPlant as well. [https://datacommons.cyverse.org/browse/iplant/home/shared/onekp_pilot](https://datacommons.cyverse.org/browse/iplant/home/shared/onekp_pilot) * The dataset analyzed by Prum et. al. available at: Prum, R.O., Berv, J.S., Dornburg, A., Field, D.J., Townsend, J.P., Lemmon, E.M. and Lemmon, A.R., 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature. * Data available from the original paper ## Sharing/Access information ## Code/Software The simulated data are generated using Simphy and with scripts given [here](https://github.com/smirarab/astral2sims) * We used [ASTRAL (posteval)](https://github.com/smirarab/ASTRAL/tree/posteval) version 4.9.1 for scoring and [ASTRAL (master)](https://github.com/smirarab/ASTRAL/tree/master) version 4.9.8 for computing the branch length of the trees. * To have posterior probabilities of branches of main species tree and 2 other alternatives we used the [posteval branch](https://github.com/smirarab/ASTRAL/tree/posteval). ``` java −Xmx2000M −jar astral.4.9.1.jar −i [GENE TREES] −q [SPECIES TREE] −t 4 ``` To compute the branch lengths of main species tree we used the MAP solution with the command master : ``` java −Xmx2000M −jar astral.4.9.8.jar −i [GENE TREES] −q [SPECIES TREE] −t 2 ``` To compute the bootstrap support of the alternative topologies we used posteval: ``` java −Xmx2000M −jar astral.4.9.1.jar −i [BS-replicates] −q [SPECIES TREE] −t 5 ```