Co-evolution Utility Programs
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README.md

Co-evolution Utilities

The Co-evolution Utilities software suite supports both conservation-based and co-evolutionary analyses of multiple sequence alignments (MSAs). Conserved positions are amino acid positions that retain the same amino acid throughout evolution. Co-evolving positions are pairs of sites that mutate in a coordinated manner throughout evolution.

The software provides support for:

  • Differential conservation analysis among the subfamilies of homologous proteins
  • Automated co-evolutionary analyses (with 5 algorithms) using an "ensemble-average" treatment of the MSA
  • Comparison of co-evolution scores among homologous protein subfamilies
  • Mapping MSA column numbers to a given protein’s amino acid positions
  • Generation of shuffled MSAs for determining and subtracting the ”noise” from evolutionary data
  • Unthresholded analyses of co-evolutionary scores (Jaccard analysis)
  • Centrality analysis of unthresholded, weighted networks created from co-evolutionary scores

The suite was used as part of Parente and Swint-Kruse (2013). Multiple Co-Evolutionary Networks Are Supported by the Common Tertiary Scaffold of the LacI/GalR Proteins. PLoS ONE. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084398

For detailed instructions, please see README.pdf.