NAME
prune-tree.pl - Prune tips from TREE files based on id lists
VERSION
version 0.240390
USAGE
prune-tree.pl <infiles> [optional arguments]REQUIRED ARGUMENTS
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.