mrFAST: Micro Read Fast Alignment Search Tool
...d mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with...2944 days ago
2715 days ago
DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes
...of genomes between two organisms. Alternatively, by examining colinear sets of homologous genes found within a single genome, segmental genome duplications can be revealed. This softwa...2646 days ago
2483 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
...single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamles...2280 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts p...2189 days ago
1945 days ago
SDA: Long-read sequence and assembly of segmental duplications
Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences pro...1901 days ago
1512 days ago
Synteny and Rearrangement Identifier (SyRI)
...as input to SyRI. SyRI identifies syntenic path (longest set of co-linear regions), structural rearrangements (inversions, translocations, and duplications), local variations (SNPs, ind...1474 days ago