createFA2Tree

Generating phylogenetic tree from alignment file '.fa'

Usage

createFA2Tree(
  fa_file = "data/alns/pspa_snf7.fa",
  out_file = "data/alns/pspa_snf7.tre"
)

Arguments

fa_file

Character. Path to the alignment FASTA file (.fa) from which the phylogenetic tree will be generated. Default is 'pspa_snf7.fa'.

out_file

Path to the output file where the generated tree (.tre) will be saved. Default is "data/alns/pspa_snf7.tre".

Value

No return value. The function generates a phylogenetic tree file (.tre) based on different approaches like Neighbor Joining, UPGMA, and Maximum Likelihood.

Details

The alignment file would need two columns: 1. accession + number and 2. alignment. The protein homolog accession to lineage mapping + file should have

Note

Please refer to the source code if you have alternate + file formats and/or column names.

Author

Janani Ravi, MolEcologist

Examples

if (FALSE) { # \dontrun{
generate_aln2tree("pspa_snf7.fa")
} # }