CorMut provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Three methods are provided for detecting correlated mutations ,including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.
|Author||Zhenpeng Li, Yang Huang, Yabo Ouyang, Yiming Shao, Liying Ma|
|Date of publication||None|
biCkaksCodon-class: Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biCompare-class: Class "biCompare"
biCompare-methods: biCompare implement biCompare methods for comparison of the...
ckaksAA: Compute the conditional kaks(conditional selection pressure)...
ckaks-class: Class "ckaks"
ckaksCodon: Compute the conditional kaks(conditional selection pressure)...
CorMut-package: Detect the correlated mutations based on selection pressure
filterSites-methods: filterSites methods
jiAA: Compute the Jaccard index among individual amino mutations
JI-class: Class "JI"
kaksAA: Compute kaks for individual amino mutation
kaksAA-class: Class "kaksAA"
kaksCodon: Compute kaks for individual codon
kaksCodon-class: Class "kaksCodon"
miAA: Compute the mutual information among individual amino...
MI-class: Class "MI"
miCodon: Compute the mutual information among codons
plot-methods: Plot methods for CorMut package
seqFormat-methods: Process the multiple sequence alignment files