:: DESCRIPTION
CAR is an efficient and more accurate tool for assembling contigs of a prokaryotic draft genome based on a reference genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
No
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2014 Nov 28;15(1):381.
CAR: contig assembly of prokaryotic draft genomes using rearrangements.
Lu C, Chen KT, Huang SY, Chiu HT.
:: DESCRIPTION
BAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Med. 2013 Sep 13;5(9):82.
BAIT: Organizing genomes and mapping rearrangements in single cells.
Hills M1, O’Neill K, Falconer E, Brinkman R, Lansdorp PM.
:: DESCRIPTION
GRIL is a tool that can be used to identify the location of rearrangements and inversions in the backbone of a set of DNA sequences. GRIL works by identifying exactly matching regions present in all sequences under consideration and organizing them into groups of collinear regions. GRIL removes small regions of collinearity that appear unlikely to be true sequence rearrangements based on user-specified criteria such as the length of the collinear region and the percent sequence identity of the collinear region. The size of sequences that GRIL can be applied to is dependent on the amount of available memory.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Aaron E. Darling, Bob Mau, Frederick R. Blattner and Nicole T. Perna
GRIL: genome rearrangement and inversion locator
Bioinformatics (2004) 20 (1): 122-124.
:: DESCRIPTION
Bellerophon is a hybrid split-read and paired-read method for detecting and classifying interchromosomal structural variants at base-pair level.
::DEVELOPER
Computational Biology lab @ Case (CBC)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next-generation sequencing data.
Hayes M, Li J.
BMC Bioinformatics. 2013;14 Suppl 5:S6. doi: 10.1186/1471-2105-14-S5-S6.
:: DESCRIPTION
Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Diogo Pratas, Raquel M. Silva, Armando J. Pinho, Paulo J. S. G. Ferreira.
An alignment-free method to find and visualise rearrangements between pairs of DNA sequences.
Scientific Reports, 2015 (Accepted).
:: DESCRIPTION
Gremlin is an interactive visualization model for the comparative analysis of structural variation in human and cancer genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
T.M. O’Brien, A. Ritz, B.J. Raphael, and D.H. Laidlaw. (2010)
Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements.
IEEE Transactions on Visualization and Computer Graphics. vol.16, no.6, pp.918-926.
:: DESCRIPTION
UniMoG (former DCJ) is a software tool unifying five genome rearrangement distance models: double cut and join (DCJ), restricted DCJ, Hannenhalli and Pevzner (HP), inversion only and translocation only. It allows computing all of these five distances between pairs of genomes represented as sequences of oriented common blocks.
DCJ (double-cut-and-join) computes the double-cut-and-join distance between two genomes and an optimal sorting scenario that transforms one genome into the other. It operates on the most general model of genomes with a mixed collection of linear and circular chromosomes. The sorting process includes all classical rearrangement operations such as inversions, translocations, transpositions, block interchanges, fusions and fissions.
::DEVELOPER
Rafael Friesen, Julia Mixtacki, Jens Stoye
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Oct 1;28(19):2509-11. Epub 2012 Jul 18.
UniMoG–a unifying framework for genomic distance calculation and sorting based on DCJ.
Hilker R1, Sickinger C, Pedersen CN, Stoye J.
A. Bergeron, J. Mixtacki, J. Stoye.
A unifying view of genome rearrangements
Proceedings of WABI 2006, LNBI 4175, 163-173, 2006.
:: DESCRIPTION
The software DeCoLT computes adjacencies (or any type of relation, like regulation, interaction, functional relationships) between ancestral genes from gene phylogenies reconciled with a species phylogeny according to duplications, losses and lateral gene transfer. It takes as input (1) a species tree (2) a set of extant genes (3) a set of exant adjacencies (relations) between extant genes and (4) reconciled gene trees which leaves are the extant genes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2013;14 Suppl 15:S4. doi: 10.1186/1471-2105-14-S15-S4. Epub 2013 Oct 15.
Lateral gene transfer, rearrangement, reconciliation.
Patterson M, Szöllősi G, Daubin V, Tannier E.
:: DESCRIPTION
ZoomX analyzes single molecule whole genome sequencing data sets to identify long-range rearrangements.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2018 Feb 28;46(4):e19. doi: 10.1093/nar/gkx1193.
Identification of large rearrangements in cancer genomes with barcode linked reads.
Xia LC, Bell JM, Wood-Bouwens C, Chen JJ, Zhang NR, Ji HP.
:: 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
:: DOWNLOAD
:: 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.
