http://www.evolution.unibas.ch/walser/bacteria_community_analysis/2015-02-10_MBM_tutorial_combined.pdf

Alpha Diversity: within sample diversity ... Chao1 index – es(mate diversity from abundance data (importance of rare OTUs) ... Alpha Diversity: species evenness.

https://www.researchgate.net/post/How_to_interpret_Chao1_and_Chao2_values

Please advise on how can i best use the DIVERSITY OPTIONS in the software. Thanks ... The Chao1 estimator is based on the presence of the former. ..... What is the difference between alpha-diversity and beta-diversity in microbial ecology?

https://www.drive5.com/usearch/manual/alpha_diversity.html

Alpha diversity metrics · Octave plots ... Alpha diversity is the diversity in a single ecosystem or sample. ... The best-known estimator for NGS OTUs is Chao1.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC93182/

Reliable estimates of microbial diversity would offer a means to address once ..... Rarefaction curves yield the same pattern of relative diversity as Chao1; ...

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0200728

Jul 12, 2018 ... Alpha diversity of the samples was measured by observed species, the Shannon diversity, and the Chao1 index. The observed species index ...

https://joey711.github.io/phyloseq/plot_richness-examples.html

Since we are interested in alpha diversity, it is probably not a bad idea to prune OTUs ... measures=c("Chao1", "Shannon")) p + geom_point(size=5, alpha=0.7)

http://qiime.org/scripts/alpha_diversity.html

This script calculates alpha diversity, or within-sample diversity, using an OTU table. ... To perform alpha diversity (e.g. chao1) on a single OTU table, where the  ...

https://forum.qiime2.org/t/alpha-and-beta-diversity-explanations-and-commands/2282

Jan 28, 2018 ... About the Alpha and Beta Diversity Analysis Tutorial This Alpha and Beta Diversity ... Confidence interval for richness estimator, Chao1; --p-metric : chao1_ci ...

https://en.wikipedia.org/wiki/Alpha_diversity

In ecology, alpha diversity (α-diversity) is the mean species diversity in sites or habitats at a local scale. The term was introduced by R. H. Whittaker together with  ...

http://www.wernerlab.org/teaching/qiime/overview/e

In this step we'll look into alpha diversity - a measure of species richness or ... you may have a preference for Chao1, Simpson's Diversity, Shannon Index, etc.