dat2phylip: Conver the data frame to sequential PHYLIP format file

In helixcn/phylotools: Phylogenetic Tools for Eco-Phylogenetics

Conver the data frame to sequential PHYLIP format file

Description

Convert and save a data frame to sequential PHYLIP file.

Usage

dat2phylip(dat, outfile = "out.phy")

Arguments

dat	the data frame returned by read.phylip, read.fasta.
outfile	character string represents the phylip file to be generated.

Details

The output will be in sequential PHYLIP format.

Value

This is a subroutine, there is no return value.

Note

The names of the sequences should not contain white space or Punctuation characters. See regex for more details.

Author(s)

Jinlong Zhang <[e-mail]>

References

http://www.genomatix.de/online_help/help/sequence_formats.html

See Also

dat2fasta, read.fasta, read.phylip

Examples

  cat(
  ">seq_2", "GTCTTATAAGAAAGAATAAGAAAG--AAATACAAA-------AAAAAAGA",
  ">seq_3", "GTCTTATAAGAAAGAAATAGAAAAGTAAAAAAAAA-------AAAAAAAG",
  ">seq_5", "GACATAAGACATAAAATAGAATACTCAATCAGAAACCAACCCATAAAAAC",
  ">seq_8", "ATTCCAAAATAAAATACAAAAAGAAAAAACTAGAAAGTTTTTTTTCTTTG",
  ">seq_9", "ATTCTTTGTTCTTTTTTTTCTTTAATCTTTAAATAAACCTTTTTTTTTTA",
  file = "trn1.fasta", sep = "\n")

res <- read.fasta("trn1.fasta")
dat2phylip(res)
unlink("trn1.fasta")
unlink("out.phy")

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