Sentence examples for ecology package from inspiring English sources
Rarefaction curves and diversity indices were computed for each sample using Vegan package (Community Ecology Package; R package version 1.17-3 1.17-3
Rarefaction curves for diversities were estimated based on the 97 % sequence similarity threshold for OTU identification in the R ecology package vegan [ 62].
The following steps were carried out by the QIIME (Quantitative Insights into Microbial Ecology) software package (Caporaso et al. [2011]).
To address these issues, we developed the Automation, eXtension, and Integration Of Microbial Ecology (AXIOME) package and the associated graphical user interface, Axiometic.
Sequences were analysed using the quantitative insights into microbial ecology (QIIME) software package.
Shotgun processed data were denoised using AmpliconNoise [ 22] as part of the Quantitative Insights Into Microbial Ecology version 1.5.0 package [ 23], followed by chimera removal with ChimeraSlayer [ 24].
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The QIIME (Quantitative Insights Into Microbial Ecology; ver. 1.9.1) data analysis package was used for 16S rRNA data analysis.
The open source software package Quantitative Insights into Microbial Ecology (QIIME; Caporaso et al. 2010) was used to manage the analysis flow.
The remaining sequences were analyzed using the open source software package Quantitative Insights Into Microbial Ecology (QIIME) version 1.7.0 (Caporaso et al., 2010; Kuczynski et al., 2011).
Sequences generated from pyrosequencing were submitted to the open source software package Quantitative Insights into Microbial Ecology (QIIME; http//qiime.source-forge.net) for removal of low quality sequences.
