read.phylip: read phylip file

In helixcn/phylotools: Phylogenetic Tools for Eco-Phylogenetics

read phylip file

Description

read the phylip file, and store the sequences and their names in a dataframe.

Usage

read.phylip(infile, clean_name = TRUE, seq.name.length = NA)

Arguments

infile	character string for the name of the phylip file.
clean_name	logical, representing cleaning of the names will be performed.
seq.name.length	Number of characters for the sequence names, if not specified, the function will use the first white space as the identifier. All the character before the first white space will be treated as sequence names, and the rest will be treated as sequences.

Details

read.phylip accepts both interleaved and sequential phylip, the number of sequences is identified by parsing the first line of the file. Sequences and their names will be stored in a data frame.

If clean_name is TRUE, punctuation characters and white space be replaced by "_". Definition of punctuation characters can be found at regex.

Value

a data frame with two columns: (1) seq.name, the names for all the sequences; (2) seq.text, the raw sequence data.

Note

the Punctuation characters and white space in the names of the sequences will be replaced by "_".

Author(s)

Jinlong Zhang <[e-mail]>

See Also

read.fasta

Examples

  cat("6 22",
  "seq_1    --TTACAAATTGACTTATTATA",
  "seq_2    GATTACAAATTGACTTATTATA",
  "seq_3    GATTACAAATTGACTTATTATA",
  "seq_5    GATTACAAATTGACTTATTATA",
  "seq_8    GATTACAAATTGACTTATTATA",
  "seq_10   ---TACAAATTGAATTATTATA",
  file = "matk.phy", sep = "\n")

res <- read.phylip(infile = "matk.phy")
unlink("matk.phy")

helixcn/phylotools documentation built on Oct. 11, 2024, 4:11 a.m.