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AliGROOVE – visualization of heterogeneous sequence divergence



Quick facts

Project title: 
AliGROOVE – visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support
ZFMK Project lead: 


AliGROOVE determines and visualizes the content of potentially randomized sequence similarities and alignment ambiguities in multiple sequence alignments.
The AliGROOVE algorithm is an adaptation of the recently published ALISCORE masking algorithm (Misof & Misof, 2009, Kück et al., 2010). AliGROOVE summarizes site scores of profiles of sequence similarity normalized over the whole alignment length from each pairwise comparison and translates the obtained scoring distances between sequences into a similarity Matrix (Figure 1).

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Figure 1: Example Result Pairwise Sequence Similarity Matrix

AliGROOVE can be used to analyse sequence heterogeneity of concatenated supermatrices, but also to analyse the influence of heterogeneity that derives from single gene partitions. Therefore, the script is well suited for single gene analyses as well as for phylogenomic data.
In addition, AliGROOVE can tag unreliable branches of given topologies. To define the reliability of single branches, AliGROOVE calculates the average similarity between taxa which are connected by a respective branch. This tagging of branches is an indirect estimation of reliability of a subset of all possible splits guided by a topology. Calculated reliabilities of single branches are shown colorized in tree Output (Figure 2).

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Figure 2: Example Result Tree Tagging

The simple usage of the AliGROOVE program via graphical user interface facilitates the identification of potentially problematic taxa or gene partitions for users which feel uncomfortable with command line based software while the alternatively available command line version of AliGROOVE can be easily integrated into automated analysis pipelines. AliGROOVE has no maximum limit in taxon number or sequence length.

The actual version of AliGROOVE and the corresponding manual can be downloaded from GitHub:


Contact person

Head of Section
+49 228 9122-404
+49 228 9122-212
P.Kueck [at]