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=item B<-k>=<string>,
      B<--key>=<string>


=item B<-v>,
      B<--verbose>


=item B<-h>,
      B<--help>

Print a brief help message and exit.

=item B<--man>

Print the manual page and exit.

=item B<--version>

Print version information and exit.

=item B<-l>,
      B<--log>

Creates, or appends to, a generic FAST logfile in the current working
directory. The logfile records date/time of execution, full command
with options and arguments, and an optional comment.

=item B<-L [string]>,
      B<--logname=[string]>

Use [string] as the name of the logfile. Default is "FAST.log.txt".

=item B<-C [string]>,
      B<--comment=[string]>

Include comment [string] in logfile. No comment is saved by default.

=item B<--format=[format]> 		  

Use alternative format for input. See man page for "fasconvert" for
allowed formats. This is for convenience; the FAST tools are designed
to exchange data in Fasta format, and "fasta" is the default format
for this tool.

=item B<-m [dna|rna|protein]>,
      B<--moltype=[dna|rna|protein]> 		  

Specify the type of sequence on input (should not be needed in most
cases, but sometimes Bioperl cannot guess and complains when
processing data).

=back

=head1 EXAMPLES

Print alignment of 5'UTRs

=over 8

B<gbfalncut> -k --verbose t/data/AF194338.1.gb 5.UTR t/data/ArdellEtAl03_ncbi_popset_32329588.fas

=back

Print alignment of coding regions (CDS), remove sequences, degap and translate them

=over 8

B<gbfalncut> -k  t/data/AF194338.1.gb CDS t/data/ArdellEtAl03_ncbi_popset_32329588.fas | fasgrep -v "(AF194|3496)" | fastr -snD "-" | fasxl -t 6

=back

=head1 SEE ALSO

=over 8

=item C<man perlre>

=item C<perldoc perlre>

Documentation on perl regular expressions.

=item C<man FAST>

=item C<perldoc FAST>

Introduction and cookbook for FAST

=item L<The FAST Home Page|http://compbio.ucmerced.edu/ardell/FAST>"

=back 

=head1 CITING

If you use FAST, please cite I<Lawrence et al. (2014). FAST: FAST Analysis of
Sequences Toolbox.> and Bioperl I<Stajich et al.>. 

=cut