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Figure 1 | BMC Bioinformatics

Figure 1

From: Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets

Figure 1

Protocol Overview. For RCM, the original sequences and sequences recoded with reduced alphabets are used to calculate RCM-based distances which are then inputted sequentially to the Neighbor-Joining and Retree programs of the PHYLIP v3.68 package. For MSA, first, alignments are carried out using ClustalW2 with substitution matrices corresponding to each amino acid alphabet. Following bootstrap analysis with ClustalW2, Retree program is used to root the trees with midpoint rooting and to discard branch lengths. Each phylogenetic tree is then inputted to the TBC algorithm along with its attribute file that shows the expert assignment of each sequence to each family to calculate the TBC error.

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BMC Bioinformatics

ISSN: 1471-2105

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