Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assemb...long reads to optimally order and orient contigs assembled from...res for the assembly of large and complex genomes.Song Gao, Den...erformance guarantees. Genome Biology, May 2016, doi: 10.1186/s1305...ces. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb....2363 days ago
2361 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elem...ch as taxonomic information, gene names and identifiers, branch lengths,...perability between various applications and dat...2361 days ago
GPOPSIM: a simulation tool for whole-genome genetic data
GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexib...ers, especially can simulate multiple genetically correlated traits with desired genetic parameters and und...2312 days ago
AliTV—interactive visualization of whole genome comparisons
AliTV, which provides interactive visualization of whole genome alignments. AliTV reads...m the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and hig...2319 days ago
2309 days ago
PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graph...interface. Serials of algorithms and methodologies have been developed and integrated to analyze and vis...h different conservative levels, and genetic variation from pan-genome...ot in PGAP-X were shown as Fig.1 and Fig...2306 days ago
Mesquite: A modular system for evolutionary analysis
...dular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phyloge...2257 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical chall...The join between two contigs A and B is considered correct if:...genome repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take...s. https://github.com/mandricigor/repeat-aware2248 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
The k-mer Weighted Inner Product. This software implements a de no...gnment free measure of sample genetic dissimilarity which operates.... It is able to calculate the genetic dissimilarity between samples...without any reference genome, and without assembling one. De novo estimates of genetic...2180 days ago