seqFormat

seqFormat-methods


a character string specifying the format of the file: "clustal","fasta","mase","phylip","msf", refer to read.alignment function in seqinr package for details.


format


Process the multiple sequence alignment files, the results can be used for the other functional functions. Note that the reference sequence should be included as the first sequence.


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.

Zhenpeng Li

CorMut

Detect the correlated mutations based on selection pressure

seqFormat-methods function

a character string specifying the format of the file: "clustal","fasta","mase","phylip","msf", refer to read.alignment function in seqinr package for details.

Process the multiple sequence alignment files, the results can be used for the other functional functions. Note that the reference sequence should be included as the first sequence.

seqFormat-methods: Process the multiple sequence alignment files

Description

Usage

Arguments

Value

Examples