MGRA: Breakpoint graphs and ancestral genome reconstructions
MGRA (Multiple Genome Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and e...on 2 MGRA supports gene insertion and deletions in addition to genome rearrangements and allows the input genomes...2530 days ago
SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, a...2381 days ago
SimLoRD: A read simulator for third generation sequencing reads
...nerated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a late...2137 days ago
1609 days ago
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete o...1540 days ago
NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences
...ates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences...1515 days ago
Synteny and Rearrangement Identifier (SyRI)
...tifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations,...variations (SNPs, indels, CNVs etc) within syntenic and structural rearrangements, and un-aligned regions....1515 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation...1503 days ago
Sibelia: A comparative genomics tool
...ganisms. Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to...1406 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
...synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency w...s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity...994 days ago