In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the such often criticized, extent SRH violations their effects on inference tree topologies edge lengths are not well understood. Here, introduce apply maximal matched-pairs tests homogeneity to assess scale impact model 3,572 partitions from 35 published data sets. We show roughly one-quarter all analyzed (23.5%) reject...

Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating for training machine-learning applications. Many sequence simulation programmes exist, but most feature-rich tend to be rather slow, and fastest feature-poor. Here, we introduce AliSim, a new tool that can efficiently simulate biologically realistic alignments...

Abstract Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these lack the ability infer root placement estimated phylogeny. In order compensate for inability tree, researchers use external information such as using outgroup taxa or additional molecular clocks. this study, investigate utility nonreversible phylogenies...

Genomic regions that play a role in parasite defense are often found to be highly variable, with the major histocompatibility complex serving as an iconic example. Single nucleotide polymorphisms may represent only small portion of this variability, Indel and copy number variation further contributing. In extreme cases, haplotypes no longer recognized orthologous. Understanding evolution such divergent is challenging because most not visible using reference-assisted genomic approaches. Here...

A bstract Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these lack the ability infer root placement estimated phylogeny. In order compensate for inability tree, researchers use external information such as using outgroup taxa or additional molecular-clocks. this study, investigate utility non-reversible...

A bstract Phylogenetic inference typically assumes that the data has evolved under Stationary, Reversible and Homogeneous (SRH) conditions. Many empirical simulation studies have shown assuming SRH conditions can lead to significant errors in phylogenetic when violates these assumptions. Yet, many focused on extreme non-SRH represent worst-case scenarios not average dataset. In this study, we simulate datasets various degrees of using empirically derived parameters mimic real examine effects...

Abstract Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating for training machine-learning applications. Many sequence simulation programs exist, but most feature-rich tend to be rather slow, and fastest feature-poor. Here, we introduce AliSim, a new tool that can efficiently simulate biologically realistic...

Abstract In phylogenetic inference we commonly use models of substitution which assume that sequence evolution is stationary, reversible and homogeneous (SRH). Although the such often criticized, extent SRH violations their effects on tree topologies edge lengths are not well understood. Here, introduce apply maximal matched-pairs tests homogeneity to assess scale impact model 3,572 partitions from 35 published datasets. We show many (39.5%) reject assumptions, for most datasets, trees...

Genomic regions that play a role in parasite defense are often found to be highly variable, with the MHC serving as an iconic example. Single nucleotide polymorphisms may represent only small portion of this variability, Indel and copy number variation further contributing. In extreme cases, haplotypes no longer recognized homologs. Understanding evolution such divergent is challenging because most not visible using reference-assisted genomic approaches. Here we analyze case Pasteuria...