Open Source Software

This page aims to acknowledge the open source software projects that have been contributed to this resource.

CATH Tools

Our own open source software is being developed as @UCLOrengoGroup on GitHub.

Web application

  • Perl – The Perl Programming Language
  • Catalyst – MVC web application framework
  • Moose – Object system for Perl 5
  • DBIx::Class – Object relational mapper
  • BioPerl Perl tools for bioinformatics, genomics and life science

Web deployment/architecture

Web pages

  • MSAViewer – Multiple Sequence Alignment Viewer (thanks @wilzbach) 1)
  • 3Dmol.js – A modern, object-oriented JavaScript library for visualizing molecular data 2)
  • D3 – Data-Driven Documents
  • BioJS – Modern data visualizations for the web

Pipeline

  • BLAST – Basic Local Alignment Search Tool
  • HMMER3 – Biosequence analysis using profile hidden Markov models
  • MAFFT – Multiple alignment program
1) Guy Yachdav, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James Procter, Suzanna Lewis, Burkhard Rost, Tatyana Goldberg. "MSAViewer: interactive JavaScript visualization of multiple sequence alignments." Bioinformatics (2016)
2) Nicholas Rego and David Koes 3Dmol.js: molecular visualization with WebGL Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829