DoubleRecViz
SUMMARY MANUAL DOWNLOAD WEBSERVER

What is DoubleRecViz?

DoubleRecViz is a tool for visualizing and editing double reconciliations between phylogenetic trees at three levels: transcript, gene and species. DoubleRecViz makes use of an extension of the recPhyloXML model (developed for gene-species tree reconciliation) to represent joint transcript-gene and gene-species tree reconciliations. DoubleRecViz is implemented using the Dash library, which is a toolbox that provides dynamic visualization functionalities for web data visualization in Python.

DoubleRecViz takes as input one the following types of object:

  • a <doubleRecPhylo> object containing 1 species tree (<spTree> object) followed by 1 to n sets such that each set is composed of 1 reconciled gene tree (<recGeneTree> object) followed by 0 to n reconciled transcript trees (<recTranscriptTree> object).
  • a <recPhylo> object containing 1 species tree (<spTree> object) followed by 1 to n reconciled gene trees (<recGeneTree> object)
  • a <recPhylo> object containing 1 gene tree (<gnTree> object) followed by 1 to n reconciled transcript trees (<recTransTree> object)

DoubleRecViz makes use of the doubleRecPhyloXML and recTransTreeXML grammars which are extensions of the recPhyloXML and recGeneTreeXML grammars inherited from phyloXML and designed to describe reconciled gene-species tree reconciliations (detailed description of the recPhyloXML and recGeneTreeXML grammars).

Example of <doubleRecPhylo> objects for transcript-gene-species tree reconciliations, and <recPhylo> objects for a transcript-gene and gene-species tree reconciliations can be found in the testData directory of the GitHub repository.

A detailed description of the doubleRecPhyloXML and the recTransTreeXML formats can be found in the manual.