VII. Tools for tree and placement results visualisation
Most phylogenetic placements tools output their results using the "Jplace" JSON specification (FA. Matsen, 2012).
A jplace file is contains basically 2 informations:
- a newick representation of the tree to which queries were placed (with added branch labels)
- a table-like json representation of the information associated to each placement
Over the past years many tools have been developed to open and visualize the content of jplace files, both in terms of summarizing the placements statistics and in visualizing the tree itself decorated with placement results.
- Archeoteryx: one of the first tool supporting the jplace format, allows to display placements results on a tree view. (https://sites.google.com/site/cmzmasek/home/software/archaeopteryx)
- iTol: an online tool allowing to load jplace files and particulalry versatile in displaying the annotated tree in different configurations and with different metadata. (https://itol.embl.de)
- GUPPY: one the first tool specifically designed for the post-analysis and manipulation of placement results. Allows to manipulate jplace files, extract desired information (tree, subsets of placements...), to compare different samples via placement-based statistics and compute the phylogenetic diversity represented by the placements. (https://matsen.github.io/pplacer/generated_rst/guppy.html)
- GAPPAS: a faster reimplementation of many GUPPY tools but also novel functionnalities and options of tree visualisation (https://github.com/lczech/gappa/wiki)
- Phyloshift: a metabarcoding-focused tool, using placements for species identification. Contains several commands to manipulation placement results. (https://phylosift.wordpress.com/)
- ggtree: a versatile library allowing to load jplace results, plot the corresponding tree and placements and build basic statistics about the placements (https://guangchuangyu.github.io/ggtree-book/chapter-treeio.html#jplace-format).
- BoSSA: a library dedicated to the visualisation of placement results (https://cran.r-project.org/web/packages/BoSSA/vignettes/bossa-analysis.html)
- genesis: a very optimised C++ library dedicated to ML-based phylogenetic analyses with functions dedicated to phylogenetic placements visualisation and analysis (https://github.com/lczech/genesis)