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=for Euclid: dir.type:       string, dir eq 'asc' || dir eq 'desc'
    dir.type.error: <dir> must be one of asc or desc (not dir)

=item --annotate[=][<level>]

When specified, a taxonomic analysis of all nodes is carried out and the
nodes are named after their taxon at (or above) the specified taxonomic
level. This requires a local mirror of the NCBI Taxonomy database.

Available levels include: domain (or realm for viruses), kingdom, subkingdom,
superphylum, phylum, subphylum, superclass, class, subclass, infraclass,
superorder, order, suborder, infraorder, parvorder, superfamily, family,
subfamily, tribe, subtribe, genus, subgenus, species group, species subgroup,
species, subspecies, varietas, forma and 'no rank' (don't forget the quotes).

=for Euclid: level.type: string
    level.opt_default: 'missing'

=item --collapse=<level>

When specified, monophyletic nodes are collapsed exactly at the specified
taxonomic level. This requires enabling taxonomic annotation.

Two special levels are also supported: label and color. With label, subtrees
are collapsed on the various taxa of the CLS file (see C<--colorize> option
just below), whereas with color, subtrees colored in the same color are
collapsed. This allows collapsing nodes at various taxonomic levels and even
non-monophyletic nodes composed of taxa identically colored on purpose.

=for Euclid: level.type: string

=item --colorize=<scheme>

When specified, branches of the tree are colored after their taxon using the
specified CLS file. This requires enabling taxonomic annotation.

=for Euclid: scheme.type: readable

=item --taxdir=<dir>

Path to local mirror of the NCBI Taxonomy database.

=for Euclid: dir.type: string

=item --arb

Output tree in MUST pseudo-Newick ARB format [default: no].

=item --grp

Output BP/PP support values in MUST pseudo-consense GRP format [default: no].
When specified, this option also generates companion NBS files.

=item --figtree

Output tree in FigTree enhanced NEXUS format [default: no].

=item --itol

Output tree metadata for upload and vizualisation in iTOL [default: no].

=item --version

=item --usage

=item --help

=item --man

Print the usual program information

=back

=head1 AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

=head1 CONTRIBUTOR

=for stopwords Valerian LUPO

Valerian LUPO <valerian.lupo@uliege.be>

=head1 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.

=cut