supermat {phylotools}

Build PHYLIP supermatrix and RAxML partition file using aligned FASTA or PHYLIP files.

Description

Build PHYLIP supermatrix and create RAxML partition file using aligned fasta or phylip files.

Usage

supermat(infiles, outfile = "supermat.out.phy",
         partition.file = "gene_partition.txt")

Arguments

infiles

a character string vector for phylip or aligned fasta file.

outfile

the name of the PHYLIP supermatrix

partition.file

partition data summary describing the genes.

Details

Supermatrix here means a phylip file with combined aligned sequences. The missing sequences should be replaced with either "?" or "-".

Value

A list containing: (1)supermat.dat:a list containing all the data frames read by read.phylip or read.fasta (2)res.super.dat: a data frame containing the sequences and the names (3)partition.dat: summary for all the fasta or phylip files (4)partition.dat.vector: character string vector for the partition file for RAxML

Note

Punctuation characters and white space in the names of the sequences will be replaced by "_". More information can be found at regex. Type of the sequence in the RAxML partition file should be changed manually according to the manual of RAxML.

Author(s)

Jinlong Zhang <[e-mail]>

References

Kress, W. J., Erickson, D. L., Jones, F. A., Swenson, N. G., Perez, R., Sanjur, O., & Bermingham, E. (2009). Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proceedings of the National Academy of Sciences, 106(44), 18621-18626.

de Queiroz, A.and Gatesy, J. (2007). The supermatrix approach to systematics. Trends in Ecology & Evolution, 22(1), 34-41.

https://github.com/stamatak/standard-RAxML

See Also

read.fasta,read.phylip,dat2phylip,

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")

  cat("5 15",
  "seq_1     GATTACAAATTGACT",
  "seq_3     GATTACAAATTGACT",
  "seq_4     GATTACAAATTGACT",
  "seq_5     GATTACAAATTGACT",
  "seq_8     GATTACAAATTGACT",
  file = "rbcla.phy", sep = "\n")

  cat("5 50",
  "seq_2          GTCTTATAAGAAAGAATAAGAAAG--AAATACAAA-------AAAAAAGA",
  "seq_3          GTCTTATAAGAAAGAAATAGAAAAGTAAAAAAAAA-------AAAAAAAG",
  "seq_5          GACATAAGACATAAAATAGAATACTCAATCAGAAACCAACCCATAAAAAC",
  "seq_8          ATTCCAAAATAAAATACAAAAAGAAAAAACTAGAAAGTTTTTTTTCTTTG",
  "seq_9          ATTCTTTGTTCTTTTTTTTCTTTAATCTTTAAATAAACCTTTTTTTTTTA",
  file = "trn1.phy", sep = "\n")

supermat(infiles = c("matk.phy", "rbcla.phy", "trn1.phy"))
unlink(c("matk.phy", "rbcla.phy", "trn1.phy"))
unlink(c("supermat.out.phy","gene_partition.txt"))

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

cat(
  ">seq_1", "GATTACAAATTGACT",
  ">seq_3", "GATTACAAATTGACT",
  ">seq_4", "GATTACAAATTGACT",
  ">seq_5", "GATTACAAATTGACT",
  ">seq_8", "GATTACAAATTGACT",
  file = "rbcla.fasta", sep = "\n")

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

supermat(infiles = c("matk.fasta", "rbcla.fasta", "trn1.fasta"))
unlink(c("matk.fasta", "rbcla.fasta", "trn1.fasta"))

unlink(c("supermat.out.phy","gene_partition.txt"))