NAME

prune-tree.pl - Prune tips from TREE files based on id lists

VERSION

version 0.242020

USAGE

prune-tree.pl <infiles> [optional arguments]

REQUIRED ARGUMENTS

<infiles>

Path to input IDL files [repeatable argument].

OPTIONAL ARGUMENTS

--in[-strip]=<str>

Substring(s) to strip from infile basenames before attempting to derive other infile (e.g., TREE files) and outfile names [default: none].

--out[-suffix]=<suffix>

Suffix to append to (possibly stripped) infile basenames for deriving outfile names [default: none]. When not specified, outfile names are taken from infiles but original infiles are preserved by being appended a .bak suffix.

--ref-tree=<file>

Path to an optional TREE file (e.g., a supermatrix tree) that will be the target of the pruning operations [default: none]. Otherwise, each IDL file is assumed to match a similarly named TREE (.tre) file.

--from-must

Consider the input file as generated by ed/treeplot [default: no]. Currently, this switches to the legacy .lis format (instead of the modern .idl format).

--negate-list

Interpret the list as a negative list instead of a positive list [default: no]. This means that seqs corresponding to listed ids are discarded.

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.