This is the README for mAAna_tropy.pl

mAAna -> [m]ultiple [A]lignment [Ana]lyzer
tropy -> en[tropy] ~ information content

* calculates the entropy of an alignment column for a given CLUSTALW-ALIGNMENT
* can use local (-window=100) or global (-window=alilen) nucleotide frequences
* can average the entropy over a window of length '-smooth'
* can write out x (alignment position), y (entropy) data to a plain txt file
  -> '-dat=xmgrace'
* can cut out alignment fragments with an entropy greater than '-cut'
  and larger than '-minlen'
* can return these fragments in three formats
  - table of alignment fragments in tex ('-dat=tex')
    or html ('-dat=html') format
  - alignment of the concatenated alignment fragments in multi-fasta format
    -> '-conc'
  - all sequence motifs in multi-fasta format  -> '-motifs'

* can NOT handle data of the size 50 sequences x 1.000.000 alignment columns! 

fore more details read "Usage"


Get started
-----------
(for Linux)


execute mAAna_tropy:

  perl mAAna_tropy.pl

it should return the "usage" information ->


Usage
-----

  usage: mAAna_tropy.pl [OPTIONS] CLUSTALW-ALIGNMENTS
  needs: linux operating system
         Modules/alignment.pm
         Modules/footpint.pm
         Modules/exons.pm
         Modules/interval.pm
         (set "lib" to the location of the "Modules" directory
          in line 15 of mAAna_tropy.pl)
options: -h|-help get this usage message
         -Alpha=  default: ACGT (case insensitive)
         -gap=    default: -
         -maxgap= length of stretches of gaps that should be treated
                  as end gaps
         -minLet= minimum number of letters per column to do calculations,
                  default: 2
         -smooth= (odd) smoothing, default: 1 (no smoothing)
         -cut=    (floating point number) select alignment fragments
                  with higher information content
         -minlen= minimal length of alignment fragments, default: 6
         -dat=    xmgrace: write xmgrace data file to STDOUT 
                      tex: write LaTeX table to STDOUT
                           (only together with option -cut)
                     html: write HTML table to STDOUT
                           (only together with option -cut)
         -motifs  write motifs as multifasta to file: motifs.mfa
                  (only together with option -cut)
         -conc    write cocatenated fragments to fasta file: concali.fa
                  (only together with option -cut)
         -exons=  PS-FILE, exclude fragments that result from aligned exons 
         -window= length of window to calculate nt_frequence (default: alilen)
         -boot=   number of bootstraps (random alignments to generate)
                  default: 0

Troubleshooting
---------------

*1* Can't locate alignment.pm in @INC (...) at mAAna_tropy.pl line 19
    BEGIN failed--compilation aborted at mAAna_tropy.pl line 19
    
    todo: set "lib" to the location of the "Modules" directory
          in line 15 of mAAna_tropy.pl
          (use the absolute path)