====== 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 [[ https://github.com/UCLOrengoGroup | @UCLOrengoGroup ]] on GitHub.

  * [[ https://github.com/UCLOrengoGroup/cath-tools | cath-tools]] -- Protein structure comparison tools

===== Web application =====

  * [[ https://www.perl.org | Perl ]] -- The Perl Programming Language 
  * [[ https://www.catalystframework.org/ | Catalyst ]] -- MVC web application framework
  * [[ https://metacpan.org/release/Moose | Moose ]] -- Object system for Perl 5
  * [[ https://metacpan.org/pod/DBIx::Class | DBIx::Class ]] -- Object relational mapper
  * [[ https://bioperl.org | BioPerl ]] -- Perl tools for bioinformatics, genomics and life science

===== Web deployment/architecture =====

  * [[ https://varnish-cache.org | Varnish Cache ]] -- Web application accelerator
  * [[ https://httpd.apache.org | Apache HTTP ]] -- HTTP server
  * [[ http://lucene.apache.org/solr/| Apache Solr ]] -- Enterprise Search Platform

===== Web pages =====

  * [[https://github.com/wilzbach/msa | MSAViewer ]] -- Multiple Sequence Alignment Viewer (thanks [[https://github.com/wilzbach | @wilzbach]]) ((Guy Yachdav, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James Procter, Suzanna Lewis, Burkhard Rost, Tatyana Goldberg. [[ http://doi.org/10.1093/bioinformatics/btw474 | "MSAViewer: interactive JavaScript visualization of multiple sequence alignments." ]] Bioinformatics (2016) ))
  * [[https://github.com/3dmol/3Dmol.js | 3Dmol.js ]] -- A modern, object-oriented JavaScript library for visualizing molecular data (( Nicholas Rego and David Koes [[ http://doi.org/10.1093/bioinformatics/btu829 | 3Dmol.js: molecular visualization with WebGL Bioinformatics ]] (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829 ))
  * [[https://d3js.org/ | D3 ]] -- Data-Driven Documents
  * [[https://biojs.net BioJS | BioJS ]] -- Modern data visualizations for the web

===== Pipeline =====

  * [[ http://blast.ncbi.nlm.nih.gov/Blast.cgi | BLAST ]] -- Basic Local Alignment Search Tool
  * [[ http://hmmer.org | HMMER3 ]] -- Biosequence analysis using profile Hidden Markov Models
  * [[ http://mafft.cbrc.jp/alignment/software/ | MAFFT ]] -- Multiple alignment program
  * [[ https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/valdar/scorecons_server.pl | Scorecons ]] -- Scores residue conservation in a multiple sequence alignment