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T-Coffee
A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
Mirror sites:  www.tcoffee.org  Vital-IT, Swiss Institute of Bioinformatics (SIB)  IGS lab., CNRS  EBI, European Bioinformatics Institute  MAXPLANK  CORNELL  EMBNet-Spain 
ALIGNMENT
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EVALUATION
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PROCESSING
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Mirror sites:  www.tcoffee.org  Vital-IT, Swiss Institute of Bioinformatics (SIB)  IGS lab., CNRS  EBI, European Bioinformatics Institute  MAXPLANK  CORNELL  EMBNet-Spain 
Featured in
Bioinformatics for dummies
  
All these packages are opensource freeware. Download them and look for extra documentation on The Tcoffee Homepage and on my personal Homepage.

The Book Bioinformatics For Dummies contains a T-Coffee tutorial and many other online resources.

The following Text-Books can also help you interpret your results.