FAST --- FAST Analysis of Sequences Toolbox
Version 1.0. February, 2015

INTRODUCTION

The FAST Analysis of Sequences Toolbox (FAST) is a set of Unix tools
(for example fasgrep, fascut, fashead and fastr) for sequence
bioinformatics modeled after the Unix textutils (such as grep, cut,
head, tr, etc). FAST workflows are designed for "inline" (serial)
processing of flatfile biological sequence record databases
per-sequence, rather than per-line, through Unix command
pipelines. The default data exchange format is multifasta
(specifically, a restriction of BioPerl FastA format). FAST tools
expose the power of Perl and BioPerl for sequence analysis to
non-programmers in an easy-to-learn command-line paradigm.

You do not need to know Perl or BioPerl to use FAST.

UTILITIES

FAST 1.0 contains the following utilities. Each has its own man
page. FAST utilities may be classifed as for annotation, selection,
transformation, and analysis.

annotation
----------
faslen     -- annotate sequence lengths
fascodon   -- tally/annotate codon usage
fascomp    -- tally/annotate monomer frequencies
fasxl      -- translate gapped and ungapped sequences and alignments
fasrc      -- reverse complement nucleotide sequences and alignments

selection
---------
fasgrep    -- select sequence records by perl regular expressions
fasfilter  -- select sequence records by numerical values
fastax     -- select sequence records by NCBI Taxonomy IDs or names
fascut     -- select/reorder sequence record data by sequential ranges
fasuniq    -- remove duplicate sequence records from sorted data
fashead    -- select leading sequence records
fastail    -- select trailing sequence records
alncut     -- select sites based on variation and gap-content content
gbfcut     -- select sequences by regex match on GenBank features
gbfalncut  -- select sites by regex match on GenBank features

transformation
--------------
fasconvert -- convert sequences to or from from fasta format
fassort    -- sort sequence records
fastaxsort -- sort sequence records by NCBI Taxonomy IDs or names
faspaste   -- concatenate sequence record data
fastr      -- transform sequence records by characters and alphabets
fassub     -- transform sequence records by regex-based substitutions

analysis
--------
faswc      -- tally sequences and characters
alnpi      -- tally molecular population genetic statistics 

PREREQUISITES

FAST has some Perl dependencies. Once posted to CPAN, the easiest way
to install FAST with its dependencies will be by executing this
command:

	(sudo) perl -MCPAN -e 'install FAST'

You can also follow INSTALLATION instructions below, but you may need to
first run these commands to install FAST dependencies:

      	(sudo) perl -MPCAN -e 'install Sort::Key'
	(sudo) perl -MCPAN -e 'install Sort::MergeSort'
	(sudo) perl -MCPAN -e 'install Bit::Vector'
	(sudo) perl -MCPAN -e 'install Pod::Usage'

INSTALLATION

To install this module, please run the following:

	perl Makefile.PL
	make
	make test
	(sudo) make install

If you haven't installed perl-based software on your system before, or
you are having problems, please see more detailed notes in INSTALL.

GETTING STARTED

	perldoc fasgrep
	man fasgrep
 	perldoc FAST

Some usage examples in the man pages refer to data that ships with
FAST, in the installation package under t/data. Run these examples
with these data to get started right away using FAST.

DOCUMENTATION

Installation generates a man page for each utility. From the installation
directory, additional resources are in ./doc, particularly the FAST_Cookbook

SUPPORT

You can also look for information at:

    RT, CPAN's request tracker (report bugs here)
        http://rt.cpan.org/NoAuth/Bugs.html?Dist=FAST

    AnnoCPAN, Annotated CPAN documentation
        http://annocpan.org/dist/FAST

    CPAN Ratings
        http://cpanratings.perl.org/d/FAST

    Search CPAN
        http://search.cpan.org/dist/FAST/

CITING

If you use FAST please, cite the FAST project (Lawrence et al. 2015)
and Bioperl (Stajich et al. 2005). If you publish work that cites data
provided in this FAST installer, please cite the authors of this data
accordingly. For example, if you use the tRNAdb-CE data provided in
this installer, please cite: Abe T, Inokuchi H, Yamada Y, Muto A,
Iwasaki Y and Ikemura T (2014) tRNADB-CE: tRNA gene database
well-timed in the era of big sequence data. Front. Genet. 5:114. doi:
10.3389/fgene.2014.00114

VERSION AND CHANGES

1.0 -- First public release

LICENSE AND COPYRIGHT

Copyright (C) 2015 David H. Ardell

This program is free software; you can redistribute it and/or modify it
under the terms of the the Artistic License (2.0). You may obtain a
copy of the full license at:

L<http://www.perlfoundation.org/artistic_license_2_0>

Any use, modification, and distribution of the Standard or Modified
Versions is governed by this Artistic License. By using, modifying or
distributing the Package, you accept this license. Do not use, modify,
or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made
by someone other than you, you are nevertheless required to ensure that
your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service
mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge
patent license to make, have made, use, offer to sell, sell, import and
otherwise transfer the Package with respect to any patent claims
licensable by the Copyright Holder that are necessarily infringed by the
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