Tag: Divergent

AncestralClust – Cluster Divergent Sequences

AncestralClust

:: DESCRIPTION

AncestralClust is a clustering program, which is developed for clustering divergent sequences.

::DEVELOPER

Lenore Pipes @ Nielsen Berkeley Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

AncestralClust

:: MORE INFORMATION

Citation

Pipes L, Nielsen R.
AncestralClust: Clustering of Divergent Nucleotide Sequences by Ancestral Sequence Reconstruction using Phylogenetic Trees.
Bioinformatics. 2021 Oct 20:btab723. doi: 10.1093/bioinformatics/btab723. Epub ahead of print. PMID: 34668516.

MaxSSmap v1 – GPU program for Mapping Divergent Short Reads to Genomes with the Maximum Scoring Subsequence

MaxSSmap v1

:: DESCRIPTION

MaxSSmap is a GPU program with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. MaxSSmap identifies a local region of the genome followed by exact alignment.

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxSSmap

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Nov 15;15:969. doi: 10.1186/1471-2164-15-969.
MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.
Turki T1, Roshan U.

TandemSWAN – Divergent Tandem Repeats Searching

TandemSWAN

:: DESCRIPTION

TandemSWAN (Tandem Structure Word ANalyzer) is the tool for Divergent Tandem Repeats Searching.It is based on calculation of the repeat statistical significance and identifies the length of the repeated unit and the number of repetitions.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WIndows / Linux

:: DOWNLOAD

 TandemSWAN

:: MORE INFORMATION

Citation:

Bioinformatics. 2006 Mar 15;22(6):676-84. Epub 2006 Jan 10.
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.
Boeva V, Regnier M, Papatsenko D, Makeev V.

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