NAME

dndtag.pl - applies unique node labels to newick trees.

SYNOPSIS

perl dndtag.pl

[-t|--treefile <tree file>] [-n|--nexus] [-v|--verbose] [-h|--help] [-m|--man]

DESCRIPTION

The dndtag.pl program applies node labels to newick trees:

    ((A,B),C); --> ((A,B)n1,C)n2;

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.

-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 a valid newick-formatted tree file issued after the --treefile command line argument.

SEE ALSO

Rutger Vos: http://search.cpan.org/~rvosa

WARNINGS

Unknown option: ...

Meaning: Command line arguments where supplied that aren't recognized by the program.

No input, no output!

Meaning: Apparently, no input file name was specified.