ArticleBMC bioinformatics2014
AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.
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106 citing papers in PubMed.
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- Characterization of the five Amanita complete mitochondrial genome and the phylogenetic relationship with other Amanita fungi.BMC genomics · 2025Article
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- Mitogenomic Insights into Orthocladiinae (Diptera: Chironomidae): Structural Diversity and Phylogenetic Implications.Biology · 2025Article
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- Comparative analysis of mitochondrial genomes in lycoperdaceae fungi reveals intron dynamics and phylogenetic relationships.BMC genomics · 2025Article
- A Comparative Analysis and Limited Phylogenetic Implications of Mitogenomes in Infraorder-Level Diptera.International journal of molecular sciences · 2025Article
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46 more citing papers are in PubMed but not listed here.
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5 authors.
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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.
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