NAME
dndtag.pl - applies unique node labels to newick trees.
SYNOPSIS
- perl dndtag.pl
-
[-t|--treefile <tree file>] [-s|--string
'newick string'] [-n|--nexus] [-v|--verbose] [-h|--help] [-m|--man]
DESCRIPTION
The dndtag.pl program applies node labels to newick trees:
((A,B),C); --> ((A,B)Node1,C)Node2;The node labels are unique per tree. Already existing node labels are left in place. The output is written to standard out.
OPTIONS AND ARGUMENTS
- -t|--treefile <tree file>
-
A text file containing newick formatted tree descriptions.
- -s|--string
'newick string' -
A tree string, i.e. a parenthetical statement, possibly shell-escaped (e.g. on /bin/bash, this statement needs to be single quoted, on windows cmd double quoted).
- -n|--nexus
-
Output printed in nexus format.
- -h|--help|-?
-
Returns this help message.
- -v|--verbose
-
Verbose mode yields (a few) more messages.
- -m|--man
-
Opens the full documentation in perldoc format.
SUBROUTINES
check_args
Parameters: none
Checks command line arguments for sanity.
parse_file
Parameters: infile
Parses the provided input file.
main
Parameters: infile
Calls the other subroutines.
EXIT STATUS
The following exit values are returned:
0 All input files were processed successfully.
1 Invalid command line arguments.
2 No input file specified.
FILES
The program requires either a newick string or a valid newick-formatted tree file issued after the --treefile command line argument.
SEE ALSO
Rutger Vos: http://search.cpan.org/~rvosa