Sequence clustering can be viewed as a community detection problem on graphs, where nodes represent sequences and edges represent matches between related sequences. Source text: Zorita et al., 2015.

Desktop app
G T A T C G C T A Indel and… Indel and Carryforward Correction

ICC Indel and Carryforward Correction

Provides a complete software pipeline for users to analyze pyrosequencing data…

Provides a complete software pipeline for users to analyze pyrosequencing data for both library and amplicon applications. ICC is specifically designed to correct indel and carryforward and…

Desktop app
G T A T C G C T A GraphClust GraphClust

GraphClust

Compars and clusters RNAs according to sequence and structure. GraphClust…

Compars and clusters RNAs according to sequence and structure. GraphClust scales to datasets of hundreds of thousands of sequences. The quality of the retrieved clusters has been benchmarked against…

Desktop app
G T A T C G C T A SHape Aligner of… SHape Aligner of non-coding RNA developed by Keio…

SHARAKU SHape Aligner of non-coding RNA developed by Keio University

Aligns two read mapping profiles of next-generation sequencing outputs for…

Aligns two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping…

Desktop app
G T A T C G C T A QCluster QCluster

QCluster

A family of alignment-free measures, called Dq-type, that incorporate quality…

A family of alignment-free measures, called Dq-type, that incorporate quality value information and k-mers counts for the comparison of reads data. A set of experiments on simulated and real reads…

Desktop app
G T A T C G C T A SEED SEED

SEED

An efficient algorithm for clustering very large NGS sets. It joins sequences…

An efficient algorithm for clustering very large NGS sets. It joins sequences into clusters that can differ by up to three mismatches and three overhanging residues from their virtual center. It is…

Desktop app
G T A T C G C T A SlideSort SlideSort

SlideSort

A fast and exact method that can find all similar pairs from a string pool in…

A fast and exact method that can find all similar pairs from a string pool in terms of edit distance. SlideSort can find similar pairs within edit-distance d, from sequences whose length range from…

Desktop app
G T A T C G C T A Starcode Starcode

Starcode

An exact algorithm to determine which pairs of sequences lie within a given…

An exact algorithm to determine which pairs of sequences lie within a given Levenshtein distance. For error correction or redundancy reduction purposes, matched pairs are then merged into clusters of…

Desktop app
Web app
CD-HIT CD-HIT

CD-HIT

A widely used program for clustering biological sequences to reduce sequence…

A widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of…

Desktop app
G T A T C G C T A Rainbow Rainbow

Rainbow

Provides an ultra-fast and memory-efficient solution to clustering and…

Provides an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a…

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