AliGROOVE – visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support

Abstract

BackgroundMasking of multiple sequence alignment blocks has become a powerful method to enhance the tree-likeness of the underlying data. However, existing masking approaches are insensitive to heterogeneous sequence divergence which can mislead tree reconstructions. We present AliGROOVE, a new method based on a sliding window and a Monte Carlo resampling approach, that visualizes heterogeneous sequence divergence or alignment ambiguity related to single taxa or subsets of taxa within a multiple sequence alignment and tags suspicious branches on a given tree.ResultsWe used simulated multiple sequence alignments to show that the extent of alignment ambiguity in pairwise sequence comparison is correlated with the frequency of misplaced taxa in tree reconstructions. The approach implemented in AliGROOVE allows to detect nodes within a tree that are supported despite the absence of phylogenetic signal in the underlying multiple sequence alignment. We show that AliGROOVE equally well detects heterogeneous sequence divergence in a case study based on an empirical data set of mitochondrial DNA sequences of chelicerates.ConclusionsThe AliGROOVE approach has the potential to identify single taxa or subsets of taxa which show predominantly randomized sequence similarity in comparison with other taxa in a multiple sequence alignment. It further allows to evaluate the reliability of node support in a novel way.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-294) contains supplementary material, which is available to authorized users.

The phylogeny of Galerucinae (Coleoptera: Chrysomelidae) and the performance of mitochondrial genomes in phylogenetic inference compared to nuclearrRNAgenes

“…Heterogeneity of sequence composition of mitochondrial genomes for different data sets. The pairwise Aliscore (Kück et al., ) values are represented by coloured squares. The scores range from −1 indicating full random similarity (dark blue), to +1 indicating nonrandom similarity (bright orange).…”

“…Substitution saturation of different genes was tested in DAMBE5 with the GTR model selected as a reference model (Xia, ). The heterogeneity of sequence divergence within data sets relative to an external reference (outgroup) sequence was analysed with AliGROOVE (Kück et al., ) with the default sliding window size. The method compares the pairwise sequence divergence of individual terminals with terminals outside of the focal group, against the same measure of divergence over the entire data matrix.…”

Genome analysis revealed novel genotypes and recombination of the human parechoviruses prevalent in children in Eastern China

“…A phylogenetic tree with 1000 bootstrap resamples of the alignment data sets was generated using the neighbor-joining method in MEGA5.0 [21]. Sequence divergence based on the complete genome of HPeVs was analyzed using AliGROOVE software [22]. The scores were ranging from −1, indicating full random similarity, to +1, non-random similarity.…”

Data on taxonomic status and phylogenetic relationship of tits

“…Four datasets, A: the first and second sites of protein-coding genes, B: protein-coding genes with the third sites not employing RY-coding method, C: 37 mitochondrial genes with the third sites of protein-coding genes not using RY-coding method plus one control region, D: five nuclear segments, were used to analyze the heterogeneity in AliGROOVE [5], and the results can be found in Fig. 3.…”

“…The best schemes were analyzed in Partitionfinder v1.1.1 [4]. The heterogeneity was inferred with AliGROOVE [5]. The gene trees based on six datasets (one mitochondrial dataset and five nuclear segments) were constructed in RAxML 7.0.3 [6].…”