# Amino Acid Substitution Effect Analyser

## Documentation for package ‘aaSEA’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

AAindex | A data frame of 533 amino acid properties from AAindex.
corSubFile | A data frame of correlated sites.
Cruciani | A data frame of 3 Cruciani properties for 20 amino acids.
Fasgai | A data frame of six Fasgai vectors for 20 amino acids.
getAASub | Get amino acid substitutions from multiple sequence alignment
getCorPropChange | Get property changes associated with correlated substitutions
getCorSites | Get correlated sites with substitutions
getPropChange | Get wild type and substituted amino acid properties and associated property changes
getPropCorr | Get amino acid property wise correlations of co-evolving columns of a multiple sequence alignment
getTopSub | Get sites with more than one-correlated substitutions other than conserved amino acids at that position
Kidera | A data frame of 10 Kidera factors for 20 amino acids
matEncode | Function to encode Correlated columns of alignment matrix with desired properties
plotCorNet | simple interactive network diagram of correlated substitution pairs
plotCorSubChanges | Plot co-evolving sites with selected property correlations
plotMultiSubChange | Plots heat map of multiple substitution associated changes per site
plotSingleSubChange | Plots single substitution change histogram
startSeaShiny | Title Enables to start and run the app