Directory structure:

directory                 explanation
-----------------------+------------------------------
  ReadMe.txt           |  This file.
  generate/            |  DNAgen - generate artificial DNA-sequences.
  lib/                 |  Various libraries (dnaio, align, cliques, ...).
  profile/             |  ProfAlign - profile alignment (used by ComAlign).
  combine/             |  ComAlign - combining profile alignments.
  results/             |  Details on the results used in the article.
    dna                |    The nucleotide cost-file used by MSA.
    22_5SRNA_sequences |    The 22 5S RNA sequences that were used in
                       |      experiment 2.
    10_5SRNA_sequences |    The subset of 10 sequences that seemed to
                       |      build a family.
    ComAlign_output_22 |    ComAlign's output on the 22 5S RNA sequences
                       |      (1000 iterations).
    MSA_output_10      |    MSA's output on the 10 5S RNA sequences.
    ComAlign_output_10 |    ComAlign's output on the 10 5S RNA sequences
                       |      (10,000 iterations).