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Algorithms to compute DNA complexity
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== SeqComplex == This is a collection of methods to compute the composition and complexity of a DNA sequence(s) from a Fasta file. The SeqComplex.pm is a Perl Module containing implementations for each complexity measure. Additionally, several tools are provided which utilitize this module. They include: (1) compSeq.pl compute the methods in a windowed mode. (2) profileComplexSeq.pl compute the methods using the whole sequence. (3) gatherStats.pl: Example script to run all methods in windowed mode and save raw data for later processing. (4) displayStats.pl: Example script to read in raw data from gatherStats.pl and display as either a table or a Google Charts HTML file. Computed methods *gc: C+G content *gcs: C+G skew *cpg: CpG skew *cwf: Complexity by Wootton & Federhen *ce: Entropy *cz: Complexity as compression ratio (using Gzip) *cmN: Complexity as Markov model size of N *ctN: Trifnov's complexity with order N *clN: Linguistic complexity with order N Additonal methods *ats: A+T skew *ket: Keto skew *pur: Purine skew Copyright (C) 2009-2015 by Juan Caballero [email@example.com] All code is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.8 or, at your option, any later version of Perl 5 you may have available.