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Figure 1 | BMC Bioinformatics

Figure 1

From: SplitTester : software to identify domains responsible for functional divergence in protein family

Figure 1

The algorithm for the tree-based method to identify protein functional domains. Multiple amino acid sequences alignment is used as an input file. Phylogenetic trees from different windows of the alignment are generated by the neighbor-joining method. For each window, the program determines whether the tree from the local sequence (split cluster) matches a predefined functional split. If the split cluster is consistent with their functional split, the sequence window is a candidate for carrying out that function. The program is iterative and starts with very small windows (i.e. three amino acids), which gradually increase until the window size equals the length of the protein alignment.

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