nbase: Number of bases

In fmichonneau/chopper: Alignment Manipulations and Data Preparation for Phylogenetic Analyses

Description

Calculates the number of base pairs in each sequence of an alignment.

Usage

nbase(file, gap = "-", format = "fasta", ...)

Arguments

file	A file with DNA sequences
gap	The character(s) used as gaps in the file
format	The file format of the alignment
...	Additional parameters to be passed to read.dna

Details

The argument gap should be a valid regular expression whose value is substituted (by gsub) into empty characters. The remaining is the base pairs making up the sequences.

Value

a named vector indicating the number of non-gap characters found in each sequence.

Author(s)

Francois Michonneau

fmichonneau/chopper documentation built on May 16, 2019, 1:43 p.m.