Process the multiple sequence alignment files

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Description

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.

Usage

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seqFormat(x, format = c("clustal","fasta","mase","phylip","msf"))

Arguments

x

multiple sequence alignment files

format

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

Value

A vector of sequences with names is returned.

Note

To ensure an exact result, the reference sequence should be included in the alignment as the first sequence.

Author(s)

Zhenpeng Li

Examples

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examplefile=system.file("extdata","PI_treatment.aln",package="CorMut")
example=seqFormat(examplefile)