Clustering
| Name | Short Description | Language |
| AbundanceBin | AbundanceBin binning tool (Wu et al, 2011) (Generated by PluGen) | C++ |
| AffinityPropagation | Affinity Propagation (Frey and Dueck, 2007) | Python |
| CDHit | CD-Hit (Li and Godzik, 2006) | C++ |
| CKMeans | CKMeans (Wang and Song, 2011) | R |
| ClusterCount | Number of clusters in a network above a threshold in size | Python |
| ClusterMeans | Mean edge weight between all clusters of a network | R |
| ClusterPathways | Given a set of clusters of taxa, find all metabolic pathways shared by node pairs within the cluster | Python |
| ClusterStd | Edge standard deviation between all clusters of a network | R |
| Community | Information on the local community of a target. | Python |
| CommunityDetection | Girvan-Newman algorithm for community detection in a network (Girvan and Newman, 2002) | Python |
| Core | Core taxa community statistics | R |
| Dendogram | Dendogram-based clustering (Forina et al, 2002) | R |
| Enterotypes | Find enterotypes within a set of samples (Arumugam et al, 2011) | R |
| FCluster | FCluster (Quince et al, 2011) | C++ |
| GMM | Gaussian Mixture Model (Rasmussen, 1999) | R |
| GOCluster | Cluster using Gene Ontology (Thomas et al, 2022) | R |
| Hierarchical | Hierarchical clustering (Sibson, 1973) | R |
| HMM | Hidden Markov Model (Liu and Li, 2017) | R |
| Infomap | Infomap (Edler et al., 2017) algorithm for community detection (Generated by PluGen) | C++ |
| KMeans | KMeans clustering (MacQueen, 1967) | R |
| LinClust | Linear-Time Clustering (Steinegger and Soding, 2018) | C++ |
| Louvain | Louvain Clustering (Blondel et al, 2008) | Python |
| MaxBin | MaxBin (Wu et al, 2014) software for binning reads (Generated by PluGen) | C++ |
| MCL | Markov Clustering (van Dongen, 2000) | R |
| MClust | MClust (Scrucca et al, 2016) | R |
| MergeClusters | Merge two clusters | R |
| MetaBAT | MetaBAT (Kang et al, 2015) (Generated by PluGen) | C++ |
| MetaCluster | MetaCluster (Yang et al, 2010) (Generated by PluGen) | C++ |
| ModularityMaximization | Modularity Maximization Algorithm For Clustering Level | Python |
| MUSCLE | MUltiple Sequence Comparison by Log-Expectation (MUSCLE) (Edgar et al, 2004) alignment tool | C++ |
| PAM | Partition Around Medoids (PAM) clustering (Kaufman and Rousseeuw, 1987) | R |
| PICRUSt | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) (Lamille et al, 2013) | C++ |
| PrefixSuffix | Prefix-Suffix algorithm of Qiime (Edgar et al, 2010) | C++ |
| PyNAST | PyNAST clustering (Caporaso et al, 2010) | C++ |
| Radial | Radial clustering (Agrafiotis et al, 2007) | R |
| RGI | Cluster by Resistance Gene Identifier (RGI) | Perl |
| RivalClub | Find rival clubs in a network (Fernandez et al, 2015) | Python |
| SCIMM | Sequence Clustering with Interpolated Markov Models (Kelley and Salzberg, 2010) | C++ |
| SharedNN | Shared nearest-neighbor | C++ |
| SIMLR | SIMLR (Wang et al, 2017) | R |
| SortMerna | SortMerna (Kopylova et al, 2014) | C++ |
| Spectral | Spectral Clustering (Meila and Shi, 2001) | Python |
| SumaClust | SumaClust (Mercier et al, 2014) | C++ |
| SWARM | SWARM (Mahe et al, 2014) | C++ |
| SynerClust | SynerClust (Georgescu et al, 2018) orthologue clustering tool | C++ |
| Tightness | Various tightness measurements for a set of network clusters | R |
| TightnessStatistics | Mean and standard deviation of cluster tightness | Python |
| Trie | Trie algorithm of Qiime (Edgar et al, 2010) | C++ |
| UClust | UClust (Edgar et al, 2010) | C++ |
| UPARSE | UPARSE (Edgar, 2013) algorithm | C++ |
| USearch | USearch (Edgar et al, 2010), adds filtering steps to UClust | C++ |
| VClust | Clustering with vsearch (Rognes et al, 2016) | C++ |
| VSearch | VSearch algorithm (Rognes et al, 2016) for nucleotide-based alignments (Generated by PluGen) | C++ |
| Waltman | Community detection (Waltman and van Eck, 2013) | R |
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