1.39.5
mothur
set -o pipefail; export TERM=vt100;
anderberg - Community Membership Similarity the Anderberg similarity coefficient
braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient
canberra - Community Structure Similarity
gower - Community Structure Similarity
hamming - Community Membership Similarity
hellinger - Community Structure Similarity
jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient
jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness
jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses
jsd
kulczynski - Community Membership Similarity the Kulczynski similarity coefficient
kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient
kstest - Community Membership Similarity Kolmogorov-Smirnov test
lennon - Community Membership Similarity the Lennon similarity coefficient
manhattan - Community Structure Similarity
memchi2 - Community Membership Similarity
memchord - Community Membership Similarity
memeuclidean - Community Membership Similarity
mempearson - Community Membership Similarity
morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient
ochiai - Community Membership Similarity the Ochiai similarity coefficient
odum - Community Structure Similarity
rjsd
sharedace - Shared community richness the two sample shared ACE richness estimator
sharednseqs - Utility the number of sequences in two samples
sharedobserved - Utility the number of sequences in two samples
sharedsobs - Shared community richness the observed richness shared between two or more samples
sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator
soergel - Community Structure Similarity
sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient
sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness
sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses
spearman - Community Structure Similarity
speciesprofile - Community Structure Similarity
structchi2 - Community Structure Similarity
structchord - Community Structure Similarity
structeuclidean - Community Structure Similarity
structkulczynski - Community Structure Similarity
structpearson - Community Structure Similarity
thetan - Community Structure Similarity the Smith theta similarity coefficient
thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient
whittaker - Community Membership Similarity the Whittaker similarity coefficient
Opticlust method
Furthest neighbor
Nearest neighbor
Average neighbor
Abundance-based greedy clustering (agc)(VSEARCH)
Distance-based greedy clustering (dgc)(VSEARCH)
Matthews correlation coefficient (mcc)
Sensitivity
specificity
true positives + true negatives
false positives + false negatives
true positives
true negative
false positive
false negative
f1score
accuracy
positive predictive value
negative predictive value
false discovery rate
Singleton
Oneotu
simple
detail
savelog
10.1128/AEM.01541-09
@book{mccune2002analysis,
title={Analysis of ecological communities},
author={McCune, Bruce and Grace, James B and Urban, Dean L},
volume={28},
year={2002},
publisher={MjM software design Gleneden Beach, OR}
}
@misc{legendre1998numerical,
title={Numerical Ecology, Volume 24, (Developments in Environmental Modelling)},
author={Legendre, Pierre and Legendre, Louis},
year={1998},
publisher={Elsevier Science Amsterdam, The Netherlands}
}