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Figure 6 | BMC Bioinformatics

Figure 6

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

Figure 6

AliGROOVE example results of MAFFT realigned 15-taxon simulation tests (simulation setup C). AliGROOVE similarity scores and identified branch reliability of best Maximum Likelihood (ML) topologies as well as the obtained overall ML reconstruction success for four different branch length conditions of a 15-taxon topology (Figure 4) under the GTR model of sequence evolution used for data simulation and tree reconstruction. Realigned (MAFFT) data sets have been simulated with indel events and analysed by AliGROOVE without -N option (indel events are treated as fifth character state) or with -N option (indel events treated as ambiguous characters).

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