Welcome to alignlib.

alignlib is free software. Please see the file COPYING for details.
For documentation, please see the files in the doc subdirectory.
For building and installation instructions please see the INSTALL file.


TODO:

1. use templates for ImplAlignataSet/ImplAlignataHash.
2. implement a generic scoring system (Scoror) (for example for
   ImplFragmentorDiagonals()
3. for Dots -> check renormalisation of row/col, if not starting
  from 1
4. create makeAlignataRandom()
5. add Alignator->calculateMaxScore(); = alignment without backtracing
6. Rendering: make generic palettes

7. nicer way of dealing with masked residues and gaps in profile-sequence
comparison.
8. Alignata: add specialized implementations for removeRow/ColRegion()

9. make sure, that Alignata-iterators are not leading to segmentation faults
  for empty alignments (e.g. try AligantaVector.Clear and then try to get iterators)


Version 0.2.0: updated for SWIG 1.3.24 and new automake.