mega: Read and Write MEGA
In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

mega	R Documentation

Read and Write MEGA

Description

Read and write MEGA formatted files.

Usage

read.mega(file)

write.mega(
  g,
  file = NULL,
  label = NULL,
  line.width = 60,
  locus = 1,
  as.haplotypes = TRUE
)

Arguments

`file`	a MEGA-formatted file of sequences.
`g`	a gtypes object.
`label`	label for MEGA filename (.meg). If `NULL`, the gtypes description is used if present.
`line.width`	width of sequence lines.
`locus`	number or name of locus to write.
`as.haplotypes`	output sequences as haplotypes? If `TRUE`, contents of `@sequences` slot are returned - treated as if they were haplotypes. If `FALSE`, one sequence per individual is returned.

Value

for read.mega, a list of:

title: title of MEGA file
dna.seq: DNA sequences in DNAbin format

Author(s)

Eric Archer eric.archer@noaa.gov

References

Sudhir Kumar, Glen Stecher, and Koichiro Tamura (2015) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0. Molecular Biology and Evolution (submitted). Available at: http://www.megasoftware.net

EricArcher/strataG documentation built on May 17, 2024, 12:41 p.m.