List of potential Jalview projects

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Below is a list of past, present and future Jalview SOC project ideas. You should also check out the feature and enhancement requests at The Jalview Issue Tracker.

Extending Jalview's support for handling RNA

This is described on the 2011 Summer of Code.

Improved support for similarity and substitution matrices in Jalview

Rationale 

Matrices are ubiquitous in Phylogenetic analysis: substitution matrices provide score models for calculating and evaluating sequence alignments, and for generating the similarity matrices used in simple tree calculations. However, Jalview doesn't allow the user to change the substitution matrix used for any of its calculations, and doesn't provide a way of importing or exporting similarity matrices that are used for building trees.

Approach 

Implement parsers for commonly used matrix file formats (such as substitution matrices provided by AAindex and evolutionary distance matrices calculated by PHYLIP), and extend Jalview's user interface to allow new substitution matrices to be imported and used to calculate similarity matrices, trees, and alignment quality scores.

Challenges 
  • Implementing a new first class data type in an interactive tool for visualization and analysis
Degree of difficulty and needed skills 
  • Easy to Medium Difficulty
  • Java (file handling, parsing)
  • Basic understanding of phylogenetic analysis and sequence analysis algorithms
  • User interface development experience would be helpful but not essential


Teaching Jalview to work with PhyloXML and NeXML

Rationale 

PhyloXML and NeXML provide new standards for the storage and exchange of phylogenetic data and analysis results, and it is important that tools like Jalview support them.

Approach 

Introduce support for the import and export of trees and alignments in Jalview as either or both phylogenetic XML standards, utilising any existing NeXML or phyloXML java libraries (e.g. for NeXML, see here). Further steps could include adding support in Jalview for handling the rich phylogenetic tree annotation capabilities that these formats provide.

Challenges 
  • extending Jalview's existing tree and provenance data model for NeXML and phyloXML
  • adding new phylogenetic visualization features to a basic rectangular tree viewer
Degree of difficulty and needed skills 
  • Easy to Medium Difficulty
  • Java (file handling, parsing)
  • Basic understanding of phylogenetic analysis and sequence analysis algorithms
  • User interface development experience would be helpful but not essential