CODE2ALN - the tutorial
A short and simple guide for first usage of code2aln.

Code2aln produces multiple nucleic acid alignments using information
on coding and non-coding regions as part of the scoring function. It
is very easy to use.

Together with the source code you have got an example data set that
can be processed as a test case. The results you get can be compared
to the results made available together with the source code.

1. If you have not done this already, the first step is to compile
   the code: Change to the directory where the code files lie and type

   make

   You get the executable file 'code2aln'.

2. Code2aln reads the input nucleic acid sequence files as arguments.
   See the manual page 'code2aln.1'. The example data set is in
   Pearson's format. Type

   code2aln test.seq

   to start the alignment of the test data set. Please wait a few
   minutes until the alignment is done.

3. The program produces some information to 'stdout' concerning the
   scores of the particular partial (pairwise and cluster) alignments.
   Compare this output to the contents of the file 'stdout.txt' in the
   subdirectory './Output'. There should be no difference.

4. Code2aln detects all theoretically possible open reading frames
   which have a minimal length of 300 or one fifteenths of the sequence
   length. And it extracts all information about open reading frames and
   exons from the files when you are aligning sequences in GenBank files.
   You can see the arrangement of the coding regions as PostScript output
   in the file 'ORF.ps'. The file 'ORF.ps' in the subdirectory
   './Output' should show the same (the date of generation differs).

5. Information about the aligned sequences and their coding regions is
   also written in the file 'info.ral'. The contents should be the same
   as in the file './Output/info.ral'.

6. The file 'cluster.txt' gives a representation of the guide tree that
   determines the order of the profile alignments. The file should be the
   same as the example in './Output/cluster.txt'.

7. The final alignment is written to the file 'aln.aln'. This file should
   be the same as the example in './Output/aln.aln' exept the first line
   which shows the date of generation.

You might compare the resulting alignment with the results of some other
alignment algorithms like 'clustalw'. You should see that code2aln
produces less gaps with a much higher fraction of gaps that can be
divided by 3 which shows the strong tendency of code2aln not to disrupt
codons within coding regions.

You can use various types of input file formats, one or more sequences
per file, and 18 types of codon tables. See the manual page for further
information.

Have a good aligning ;)

