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  | AlignWise |
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AlignWise is designed to identify biologically relevant protein-coding regions whilst correcting for frame-shifts. It does this using homology, specifically BLAST searches and multiple alignments, as well as the GeneWise algorithm. It assumes that all frame-shifts located within the ORF to be sequencing errors that require correction. Use AlignFS with caution if this assumption is not true. We do not recommend using AlignWise on data generated from high-error sequencing methods, such as nanopore.


** INSTALLATION **

Simply install the required dependencies:

 - MUSCLE (in PATH as 'muscle')
 - BLAST+ (in PATH as 'blastx' and 'blastn')
Perl Modules
 - BioPerl
 - Parallel::ForkManager
 - Genewise (in PATH)


** RUNNING INSTRUCTIONS ** 

Simply type

 $ ./AlignWise.pl [filename]

To get help and further information on the running options:

 $ ./AlignWise.pl -h


** CONTACT AND CITATION **

Please cite:
AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts 
Evans  T, Loose  M
BMC Bioinformatics 2015, 16:376 (9 November 2015)

For any enquiries or bug reports please email teri.evans@nottingham.ac.uk