Scripts and data sets associated with: On testing homogeneity of the evolutionary process using alignments of homologous sequences

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 > 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.