jMSA project: scoring multiple sequence alignments in Java

jMSA is a collaborative project of the students of the “Programación Avanzada in Bionformatics” subject (Health Engineering degree, University of Málaga). The project focuses on providing a set of scores for the multiple sequence alignment (MSA).

Index:

• Multiple sequence alignment
• Installation
• Tools for multiple sequence alignment
  • 1. Progressive alignment construction
  • 2. Iterative methods
  • 3. Consensus methods
  • 4. Hidden Markov models
  • 5. Phylogeny-aware methods
  • 6. Motif finding
  • 7. Non-coding multiple sequence alignment
• How to score an MSA
• Scores
  • Star
  • Sum of pairs
  • Percentage of non-gaps
  • Percentage of totally conserved columns
  • Entropy
• Subtitution Matrix
  • Theoric base
  • Class structure
• Utils
• Examples
  • Example Group 1
  • Example Group 2
  • Example Group 3
  • Example Group 5
  • Example Group 8