dd_detection – Detecting Dispersed Duplications in High-Throughput Sequencing Data

dd_detection

:: DESCRIPTION

dd_detection is a tool for finding dispersed duplications (DDs) in high throughput sequencing data.

::DEVELOPER

dd_detection team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • samtools
  • C++ compiler

:: DOWNLOAD

 dd_detection

:: MORE INFORMATION

Citation:

Detecting Dispersed Duplications in High-Throughput Sequencing Data using a Database-Free Approach.
Kroon M, Lameijer EW, Lakenberg N, Hehir-Kwa JY, Thung DT, Slagboom PE, Kok JN, Ye K.
Bioinformatics. 2015 Oct 27. pii: btv621.

DupLoCut – Duplication Loss Phylogeny by Cutting Planes

DupLoCut

:: DESCRIPTION

DupLoCut computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

  DupLoCut

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Sep;20(9):643-59. doi: 10.1089/cmb.2013.0057.
The duplication-loss small phylogeny problem: from cherries to trees.
Andreotti S1, Reinert K, Canzar S.

wgd – Whole Genome Duplication analysis in Python

wgd

:: DESCRIPTION

wgd is a Python package and command line interface (CLI) for the analysis of whole genome duplications (WGDs). wgd implements methods for constructing Ks distributions starting from a CDS fasta file, tools for intra-genomic synteny analysis and methods for modeling and visualizing Ks distributions.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Python

:: DOWNLOAD

wgd

:: MORE INFORMATION

Citation:

Zwaenepoel, A., and Van de Peer, Y.
wgd – simple command line tools for the analysis of ancient whole genome duplications.
Bioinformatics., bty915, https://doi.org/10.1093/bioinformatics/bty915

DRIMM – Duplication and Rearrangement in Multiple Mammals

DRIMM

:: DESCRIPTION

DRIMM algorithm extends the GRIMM-Synteny (Genome Rearrangements in Men and Mice) algorithm towards the problem of identifying the synteny blocks in highly duplicated genomes.

::DEVELOPER

Son K. Pham  and Pavel A. Pevzner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 DRIMM-Synteny

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Oct 15;26(20):2509-16. Epub 2010 Aug 24.
DRIMM-Synteny: decomposing genomes into evolutionary conserved segments.
Pham SK, Pevzner PA.