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132. Oksanen J, Blanchet FG, Kindt R, Legendre P, O'hara RB, Simpson GL, et al. Vegan: community ecology package. R package version 1.17-4. URL http://CRAN R-project org/package = vegan. 2010.

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134. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39(suppl):W29–37.

135. Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst Biol. 2019;68:365–9.

136. Czech L, Barbera P, Stamatakis A. Genesis and Gappa: library and toolkit for working with phylogenetic (placement) data. bioRxiv. 2019; https://www.biorxiv.org/content/10.1101/647958v1 abstract.

137. Louca S, Doebeli M. Efficient comparative phylogenetics on large trees. Bioinformatics. 2018;34:1053–5.

138. Ye Y, Doak TG. A parsimony approach to biological pathway reconstruction/ inference for genomes and metagenomes. PLoS Comput Biol. 2009;5: e1000465.

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