DOI: 10.5061/dryad.n8pk0p2xv
title: Scripts and data sets associated with: On testing homogeneity of the evolutionary process using alignments of homologous sequences

description: In 2019, Genome Biology and Evolution (11:3341-3352) published three
 statistical tests for assessing whether alignments of genome sequences
 violate the phylogenetic assumption of evolution under homogeneous
 conditions. The new tests extend the matched-pairs tests of symmetry,
 marginal symmetry, and internal symmetry for alignments of n = 2
 homologous sequences of nucleotides or amino acids to cases where
 alignments of n &gt; 2 sequences are considered. Here we discuss the
 limitations of these new tests and then outline alternative approaches,
 which permit formal testing of multiple hypotheses (i.e., by controlling
 either the family-wise error rate or the false discovery
 rate). We show that the other approaches provide much greater
 insight into variation of the evolutionary process across lineages, via
 informal graphical methods and formal statistical procedures. Using one of
 the procedures (i.e., the Bonferroni test), we show that evolution under
 heterogeneous conditions is more prevalent than reported in the paper
 cited above and that the power of the matched-pairs tests of homogeneity
 is linked to the number of variant sites in an alignment. We
 release a new version of Homo, a program that allows for formal testing of
 multiple hypotheses and calculation of adjusted P values. Using Homo, we
 analysed an alignment of amino acids encoded by 116 flavivirus genomes,
 and reveal that these viral genomes are unlikely to have evolved under
 homogeneous conditions. To our knowledge, this is the first time that this
 has been reported for medically important Flavivirus genomes.
description: This submission contains batch scripts, sequence data, and
 protocols describing what was done in five computer-based experiments
 outlined in the manuscript with the above-mentioned title. The format of
 the submission was chosen such that it is as FAIR compliant as possible
 (i.e., that the data are Findable, Accessible, Interoperable, and
 Resuasable). In other words, the research done in the five experiment is
 reproducible. The content in folder
 Experiment_1 relates to the analysis of the performance of the Maximum
 Symmetry test. In particular, the experiment was designed to ascertain
 whether the edge lengths of a tree have an impact on the Type I error
 rate. The file named 00_README, describe the method used.
 The content in folder Experiment_2 relates to the analysis of
 the performance of the Maximum Symmetry test. In particular, the
 experiment was designed to ascertain whether the edge lengths of a tree
 have an impact on the Type II error rate. The file named 00_README,
 describe the method used. The content in folder
 Experiment_3 relates to the analysis of the performance of the Maximum
 Symmetry test. In particular, the experiment was designed to ascertain
 whether alignment length has an impact on the type II error rate. The file
 named 00_README, describe the method used. The
 content in folder Experiment_4 relates to the analysis of the performance
 of four tests concerning the global null hypothesis (H_G) of evolution
 under SRH conditions. In this case, the tests considered are
 Bonferroni's (1936) test, Hommel's (1983) test, Simes'
 (1986) test, and Naser-Khdour et al's (2019) test. The file named
 00_README, describe the method used. The content in
 folder Experiment_5 relates to the analysis of the performance of four
 tests concerning the global null hypothesis (H_G) of evolution under SRH
 conditions. In this case, the tests considered are Bonferroni's
 (1936) test, Hommel's (1983) test, Simes' (1986) test, and
 Naser-Khdour et al's (2019) test. 
 As for the genome data used in
 Experiment_2, we note: 
 The policistronically-encoded
 amino-acid sequences of 116 flavivirus genomes were retrieved from GenBank
 (https://www.ncbi.nlm.nih.gov/genbank/) and aligned using
 MAFFT v7.453
 (using ginsi mode) (Mol.
 Biol. Evol., 30:772-780). The completeness of the alignment was surveyed
 using AliStat
 v1.13 (NAR Genom. Bioinf.,
 2:lqaa024) and sites containing ambiguous characters were deleted if the
 proportion of such characters exceeded 0.2. The resulting alignment of
 3,367 sites had a completeness score
 (<em>C</em><sub>a</sub>) of 0.9880 (for details, see NAR Genom. Bioinf.,
 2:lqaa024). Model selection was done using
 ModelFinder (Nat. Methods, 14:587-589), which is
 implemented in IQ-TREE2
 v2.1.3 (Mol. Biol. Evol.,
 37:1530-1534). We only considered substitution models for viral
 polypeptides. For each model of sequence evolution considered, tree space
 was searched under the AIC and BIC optimality criteria. The rtREV+FO+I+R9
 model was optimal under the AIC and the rtREV+FO+I+R7 model was optimal
 under the BIC. Using IQ-TREE2, the same tree was identified under the two
 models. The UFBoot2 procedure (Mol. Biol. Evol.,
 35:518-522) was used to assess the consistency of the phylogenetic
 signal.
description: # Scripts and data sets associated with "On Testing Homogeneity of
 the Evolutionary Process using Alignments of Homologous Sequences"
 This DRYAD submission
 contains batch scripts, sequence data, and explanations of what was done
 in five computer-based experiments described in the manuscript with the
 above-mentioned title. * The content in folder Experiment_1 relates to the
 analysis of the performance of the Maximum Symmetry test. In particular,
 the experiment was designed to ascertain whether the edge lengths of a
 tree have an impact on the Type I error rate. * The content in folder
 Experiment_2 relates to the analysis of the performance of the Maximum
 Symmetry test. In particular, the experiment was designed to ascertain
 whether the edge lengths of a tree have an impact on the Type II error
 rate. * The content in folder Experiment_3 relates to the analysis of the
 performance of the Maximum Symmetry test. In particular, the experiment
 was designed to ascertain whether alignment length has an impact on the
 type II error rate. * The content in folder Experiment_4 relates to the
 analysis of the performance of four tests concerning the global null
 hypothesis (H_G) of evolution under SRH conditions. In this case, the
 tests considered are the Bonferroni (1936) test, the Hommel (1983) test,
 the Simes (1986) test, and the Naser-Khdour et al. (2019) test. * The
 content in folder Experiment_5 relates to the analysis of the performance
 of four tests concerning the global null hypothesis (H_G) of evolution
 under SRH conditions. In this case, the tests considered are the
 Bonferroni (1936) test, the Hommel (1983) test, the Simes (1986) test, and
 the Naser-Khdour et al. (2019) test. Jointly, the results reveal that: (a)
 the Naser-Khdour et al. (2019) test may mislead by failing to reject the
 null hypothesis that a process is stationary, reversible, and homogeneous
 (SRH) over the tree, and (b) other approaches are less likely to mislead
 users who wants to know whether their data violate the common phylogenetic
 assumption of evolution under SRH conditions. ## Description of the data
 and file structure This submission contains batch scripts, sequence data,
 and explanations of what was done in five computer-based experiments
 described in the manuscript with the above-mentioned title. The submission
 is divided into files and folders, all labelled in order of use (e.g.,
 Experiment_1, 00_README, 01_Tree_a, etc). The format of the submission was
 chosen to make it as FAIR compliant as possible. In other words, the
 research done in the five experiment is reproducible. ## Sharing/Access
 information In the case of alternative access to real sequence data used
 in this study, we refer interested parties to GenBank Links to other
 publicly accessible locations of the data: *
 GenBank accession numbers
 are included in a FASTA-formatter file, with each sequence of amino acids
 used from the Flavivirus genomes ## Code/Software All statistical analyses
 were carried out using **Homo v2.2**, which is a program written in C++.
 Heat maps were generated using a Pearl script called **HomoHeatMapper**.
 **Homo** and **HomoHeatMapper** are available from: *
 *