:: DESCRIPTION
Starcode is a DNA sequence clustering software.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2015 Jan 31. pii: btv053.
Starcode: sequence clustering based on all-pairs search.
Zorita EV, Cuscó P1, Filion G2.
:: DESCRIPTION
RepeatExplorer is a computational pipeline designed to identify and characterize repetitive DNA elements in next-generation sequencing data from plant and animal genomes.
TAREAN (TAndem REpeat ANalyzer) is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.
::DEVELOPER
Laboratory of Molecular Cytogenetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J.
TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads.
Nucleic Acids Res. 2017 Jul 7;45(12):e111. doi: 10.1093/nar/gkx257. PMID: 28402514; PMCID: PMC5499541.
Novák P, Neumann P, Macas J.
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2.
Nat Protoc. 2020 Nov;15(11):3745-3776. doi: 10.1038/s41596-020-0400-y. Epub 2020 Oct 23. PMID: 33097925.
:: DESCRIPTION
The software package SiLiX (SIngle LInkage Clustering of Sequences) implements a new algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.
::DEVELOPER
Laboratoire de Biométrie et Biologie évolutive
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ultra-fast sequence clustering from similarity networks with SiLiX.
Miele V, Penel S, Duret L.
BMC Bioinformatics. 2011 Apr 22;12:116. doi: 10.1186/1471-2105-12-116.
:: DESCRIPTION
The software package HiFiX implements the novel algorithm for HIgh FIdelity Clustering of Sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2012 Apr 15;28(8):1078-85. doi: 10.1093/bioinformatics/bts098.
High-quality sequence clustering guided by network topology and multiple alignment likelihood.
Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L.
:: DESCRIPTION
The Secator program for clustering protein sequences or coordinates data with the Secator rule on the dendrogram of hierarchical clustering.
The DPC program for clustering protein sequences or coordinates data with the DPC rule (small density between two high densities) for selecting the number of clusters
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Secator: a program for inferring protein subfamilies from phylogenetic trees.
N.Wicker, G.R.Perrin, J.C.Thierry and O.Poch
Mol.Biol.Evol., 2001, 8:1435-1441
Density of points clustering, application to transcriptomics data analysis.
N.Wicker, D.Dembele, W.Raffelsberger and O.Poch
Nucleic Acids Res., 2002, 18:3992-4000
:: DESCRIPTION
Scimm is a tool for unsupervised clustering of metagenomic sequences using interpolated Markov models.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Kelley DR, Salzberg SL.
Clustering metagenomic sequences with interpolated Markov models.
BMC Bioinformatics 11:544 2010.
