DOI: 10.5061/dryad.73n5tb36r
title: Data from: Estimating genome-wide phylogenies using probabilistic topic modeling

description: Inferring the evolutionary history of species or populations with
 genome-wide data is gaining ground, but computational constraints still
 limit our abilities in this area. We developed an alignment-free method to
 infer the genome-wide species tree and implemented it in the Python
 package TopicContml. The method uses probabilistic topic modeling
 (specifically, Latent Dirichlet Allocation or LDA) to extract ‘topic’
 frequencies from k-mers, which are derived from multilocus DNA sequences.
 These extracted frequencies then serve as an input for the program Contml
 in the PHYLIP package, which is used to generate a species tree. We
 evaluated the performance of our method with biological and simulated data
 sets: a data set with 14 DNA sequence loci from 78-92 haplotypes from two
 Australian bird species distributed in 9 populations; a second data set of
 5162 loci from 80 mammal species; and a third data set of 67317 autosomal
 loci and 4157 X-chromosome loci of 6 species in the Anopheles gambiae
 complex, and several simulated data sets. Our empirical results and
 simulated data suggest that our method is efficient and statistically
 accurate. We also assessed the uncertainty of the estimated relationships
 among clades using a bootstrap procedure for aligned sequence data and for
 k-mer data.
description: PacBio HiFi reads were generated from DNA isolated from four
 birds: a Woodhouse's Scrub-Jay (Aphelocoma woodhouseii, specimen
 MCZ:Orn:365326); a Yucatan Jay (Cyanocorax yucatanicus, specimen
 MCZ:Orn:365269); Tataupa Tinamou (<em>Crypturellus
 tataupa</em>); and White-throated Tinamou (<em>Tinamus
 guttatus</em>). DNA was isolated using Qiagen Magattract, and the
 concentration was estimated using a TapeStation. The DNA of the two
 tinamous was sequenced on a PacBio HiFi Revio DNA sequencer at the Faculty
 of Arts & Sciences Bauer Core, Harvard University, and the DNA
 from the two jays was sequenced on a PacBio HiFi machine at the DNA
 Sequencing & Genotyping Center at the University of
 Delaware.
description: # Data from: Estimating genome-wide phylogenies using probabilistic topic
 modeling
 [https://doi.org/10.5061/dryad.73n5tb36r](https://doi.org/10.5061/dryad.73n5tb36r) ## Description of the data and file structure The data consists of two fasta.gz files, which are files containing sequence data from each species. These files were converted from fastq.gz files, which is the form in which the original data was produced after post-processing from the PacBio HiFi sequencer. Fasta.gz is a standard format for DNA sequence data produced from genomes. ### Files and variables #### File: two\_birds\_Pacbio.tar.gz **Description:** The file consists of two tarred and gzipped files, as follows: * Ctat_100k_seqtk_Pacbio_reads.fasta.gz -100,000 PacBio HiFi reads from Crypturellus tataupa - Tgut_100k_seqtk_Pacbio_reads.fasta.gz - 100,000 PacBio HiFi reads from Tinamus guttatus The file was compiled with this command line: tar cvf two_birds_Pacbio.tar.gz Ctat_100k_seqtk_Pacbio_reads.fasta.gz Tgut_100k_seqtk_Pacbio_reads.fasta.gz As in a typical fasta file, each distinct sequence begins with a "&gt;" flag. The name of each sequence is arbitrary and set by the DNA sequencing machine. **Code/software** The file can be uncompressed using standard unix bash scripts. Reads were counted and measured using functions in seqkit (Shen W, Le S, Li Y, Hu F (2016) SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLOS ONE 11(10): e0163962. [https://doi.org/10.1371/journal.pone.0163962). ](https://doi.org/10.1371/journal.pone.0163962)The procedures for further analyzing the data are described in the associated publication. **Access information** Other publicly accessible locations of the data: * N/A Data was derived from the following sources: * N/A