Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Metagenomic Analysis using Phylogenetic Placement -- A Review of the
  First Decade   Phylogenetic placement refers to a family of tools and methods to analyze,
visualize, and interpret the tsunami of metagenomic sequencing data generated
by high-throughput sequencing. Compared to alternative (e. g.,
similarity-based) methods, it puts metabarcoding sequences into a phylogenetic
context using a set of known reference sequences and taking evolutionary
history into account. Thereby, one can increase the accuracy of metagenomic
surveys and eliminate the requirement for having exact or close matches with
existing sequence databases. Phylogenetic placement constitutes a valuable
analysis tool per se, but also entails a plethora of downstream tools to
interpret its results. A common use case is to analyze species communities
obtained from metagenomic sequencing, for example via taxonomic assignment,
diversity quantification, sample comparison, and identification of correlations
with environmental variables. In this review, we provide an overview over the
methods developed during the first ten years. In particular, the goals of this
review are (i) to motivate the usage of phylogenetic placement and illustrate
some of its use cases, (ii) to outline the full workflow, from raw sequences to
publishable figures, including best practices, (iii) to introduce the most
common tools and methods and their capabilities, (iv) to point out common
placement pitfalls and misconceptions,(v) to showcase typical placement-based
analyses, and how they can help to analyze, visualize, and interpret
phylogenetic placement data.

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The categories of this paper are: nucl-ex
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The categories of this paper are: supr-con
3
The categories of this paper are: physics
27
The categories of this paper are: comp-gas
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The categories of this paper are: q-alg
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The categories of this paper are: atom-ph
4
The categories of this paper are: cond-mat
31
The categories of this paper are: ao-sci
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The categories of this paper are: chao-dyn
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The categories of this paper are: hep-th
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The categories of this paper are: eess
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The categories of this paper are: gr-qc
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The categories of this paper are: astro-ph
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The categories of this paper are: hep-ph
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The categories of this paper are: acc-phys
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The categories of this paper are: quant-ph