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In the work presented by Asnicar et al, entitled “Compact graphical representation of phylogenetic data and metadata with GraPhlAn”, the authors present a software tool that allows for graphical representation of metagenetic and metagenomic hierarchichal information and the associated metadata using circular phylogeny structures.
While GraPhlAn does not represent and algorithmic advance or an implementation of analysis software with improved performance/features, it is useful as a readily usable tool for graphical representation, based on well-known standard formats and tools and perfectly fits into the metagenomics research field.
The article is well written, self-contained and appropriate figures are displayed to illustrate examples that range from simple to complex use of GraPhlAn tool using well-known public datasets.
Since the manuscript deals with a software tool there is no experimental design as such. However, authors report a methods sections that, along with widely used code repository, describe software implementation strategy adequately allowing for code examination and modification.
GraPhlAn has been implemented in both stand-alone and web-server formats, is nowadays widely used in the metagenomics research field and has been used for graphical representation in several microbiome based studies. This software tool adds to several other tools for graphical representation, such as the ones cited in the manuscript, and further facilitates visualization and hypothesis generation using metagenomics data.
Furthermore, GraPhlAn software tool is open-source, well documented and supported by the community.
The article is clearly written and lovely figures (which, given the subject, I suppose we should expect). I would have expected to see references to more of the existing literature on phylogeny visualization, specifically ETE, http://etetoolkit.org/, which shares many features with the software described here.
This paper describes a software package rather than a traditional research study. Source code is available in a public code repository with an open-source license, allowing for inspection and reuse.
The paper describes the data underlying each figure and the source database, but does not provide the actual datasets and GraPhlAn input files. For example, the data for Supplementary Figure 2 is "available in the NCBI Short Read Archive". It would be a fair bit of work to assemble the dataset and reproduce the figure, particuarly since the manuscript has very little detail about how to format metadata for display on trees.
There is an examples directory in the bitbucket repo  but these do not seem to correspond perfectly with the figures in the text.
The source code repository has good documentation and tutorials, and the authors seem responsive to users on the Google group.
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