DOI: 10.5061/dryad.nc220
title: Data from: Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus

description: Aligning sequences for phylogenetic analysis (multiple sequence alignment;
 MSA) is an important, but increasingly computationally expensive step with
 the recent surge in DNA sequence data. Much of this sequence data is
 publicly available, but can be extremely fragmentary (i.e., a combination
 of full genomes and genomic fragments), which can compound the
 computational issues related to MSA. Traditionally, alignments are
 produced with automated algorithms and then checked and/or corrected “by
 eye” prior to phylogenetic inference. However, this manual curation is
 inefficient at the data scales required of modern phylogenetics and
 results in alignments that are not reproducible. Recently, methods have
 been developed for fully automating alignments of large data sets, but it
 is unclear if these methods produce alignments that result in compatible
 phylogenies when compared to more traditional alignment approaches that
 combined automated and manual methods. Here we use approximately 33,000
 publicly available sequences from the hepatitis B virus (HBV), a globally
 distributed and rapidly evolving virus, to compare different alignment
 approaches. Using one data set comprised exclusively of whole genomes and
 a second that also included sequence fragments, we compared three MSA
 methods: (1) a purely automated approach using traditional software, (2)
 an automated approach including by eye manual editing, and (3) more recent
 fully automated approaches. To understand how these methods affect
 phylogenetic results, we compared resulting tree topologies based on these
 different alignment methods using multiple metrics. We further determined
 if the monophyly of existing HBV genotypes was supported in phylogenies
 estimated from each alignment type and under different statistical support
 thresholds. Traditional and fully automated alignments produced similar
 HBV phylogenies. Although there was variability between branch support
 thresholds, allowing lower support thresholds tended to result in more
 differences among trees. Therefore, differences between the trees could be
 best explained by phylogenetic uncertainty unrelated to the MSA method
 used. Nevertheless, automated alignment approaches did not require human
 intervention and were therefore considerably less time-intensive than
 traditional approaches. Because of this, we conclude that fully automated
 algorithms for MSA are fully compatible with older methods even in
 extremely difficult to align data sets. Additionally, we found that most
 HBV diagnostic genotypes did not correspond to evolutionarily-sound
 groups, regardless of alignment type and support threshold. This suggests
 there may be errors in genotype classification in the database or that HBV
 genotypes may need a revision.
description: Cleaned_GenBank_Files.zipHepatitis B virus GenBank files after initial data filtering steps.cleaned_genbank.zipGenome_alignments.zipSequence alignments of hepatitis B virus genomes and the S-region. Files include the manual genome alignment, de-gapped manual alignments, MUSCLE genome alignment, linearized and unlinearized PASTA alignments, and the S-region alignment.Genome_trees.zipTree files estimated from sequence alignments of hepatitis B virus genomes. Trees are best maximum likelihood (ML) trees with bootstrap support values. Includes trees based on MUSCLE, manual, and PASTA genome alignments.Genome_consensus_sequence.fastaConsensus sequence of hepatitis B virus genomes. This sequence was used as a reference for HBV manual alignments.GenomeConsensus.fastaGenotype_trees.zipTree files used for genotype occupancy tests in hepatitis B viruses. Trees estimated from manual or PASTA genome alignments. Files include .tre and .xml format.GI_Clustering.zipInitial files of hepatitis B virus sequences clustered according to GenBank GI number.Supplementary_Table_S1.xlsxPairwise comparisons of hepatitis B virus phylogenies. Tree names (based on alignment type) are listed in the first two columns. Tree incompatibility ratios (T.ratio) and Robinson-Fould distances (RF dsitance) are listed for each tree comparison and boostrap support threshold (Cutoff).hbv_supp_tableS1_compatability_rf.xlsxSupplementary_Table_S2.xlsxGenotype occupancy values for hepatitis B viruses. Genotype occupancy is the proportion of each genotype that makes up the minimum clade including all individuals of that genotype. Values are given for each tree (named according to alignment method), genotype, and bootstrap support cutoff for collapsing branches. The total number of sequences (i.e., tips in the tree) are indicated for each genotype.hbv_supp_tableS2_genotype_occupancy.xlsxSupplementary_Information.docxList of commands used in software programs for the alignment and tree estimation of hepatitis B virus sequences.hbv_suppinfo_commands.docxInitial_GenBank_Download.gbInitial GenBank download file of all hepatitis B virus sequences as of March 20, 2013.initial_genbank_download_sequences.gbS-region_trees.zipTrees estimate from S-region alignments of hepatitis B viruses. Includes the best maximum likelihood tree with bootstrap support values, and a file with the bootstrap replicates.S_region_trees.zipTotal_alignment_trees.zipTrees estimated from total alignments (genomes + fragmentary sequences) of hepatitis B viruses. Includes trees estimated from manual and UPP alignments.Total_alignments.zipSequence alignments of the total (genomes + fragmentary sequences) hepatitis B virus data set. Files include the manual alignment and both UPP alignments (manual genome alignment backbone, PASTA genome alignment backbone).