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.

Improving PhyloXML and NeXML and Jalview

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