write_paup: perpare nexus file to run paup

In dongzhuoer/mcapomorphy: Molecular Classfication based on amino acid apomorphy

Description

perpare nexus file to run paup

Usage

write_paup(fasta_file, newick_file, outgroup, output_file)

Arguments

fasta_file	string. sequence file in FASTA format. see fasta_to_nexus() for requirement of the content
newick_file	string. tree file in Newick format.
outgroup	character. name of outgroups, ' ' would be replaced by '_'
output_file	string. path to the output NEXUS file.

Details

for fasta_file, newick_file and outgroup only [[:alnum:]_] are allowed in taxon name (sequence header)

Value

NULL

Examples

temp_file <- tempfile()
write_paup(
    system.file('extdata', 'EOG090F05Z3.fasta', package = 'mcapomorphy'), 
    system.file('extdata', 'omics.tre', package = 'mcapomorphy'), 
    aves::outgroup$species, temp_file
)
## Not run: 
    system2('paup4a159', 'data-raw/EOG090F05Z3.nexus -n -u', T)

## End(Not run)

dongzhuoer/mcapomorphy documentation built on Jan. 9, 2020, 3:28 a.m.