Diversity analysis

(beta diversity: between sample diversity)



PCoA (bray-curtis)
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Principal Coordinates Analysis (PCoA) were performed using the Bray Curtis distance between samples.

Gower, J. C. (1966). Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53(3-4), 325-338.
Bray, J. R., and J. T. Curtis. (1957). An ordination of the upland forest communities of southern Wisconsin. Ecological Monographs 27:325–349.

PCoA (weighted-unifrac)
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Principal Coordinates Analysis (PCoA) were performed using the Weighted UniFrac distance between samples.

Gower, J. C. (1966). Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53(3-4), 325-338.
Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., & Knight, R. (2011). UniFrac: an effective distance metric for microbial community comparison. The ISME journal, 5(2), 169-172.

PCoA (unweighted-unifrac)
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Principal Coordinates Analysis (PCoA) were performed using the Unweighted UniFrac distance between samples.

Gower, J. C. (1966). Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika, 53(3-4), 325-338.
Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J., & Knight, R. (2011). UniFrac: an effective distance metric for microbial community comparison. The ISME journal, 5(2), 169-172.