Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but s...2500 days ago
CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-a...accuracy and general applicability of BLAST with computational efficiency, accessibility, an...an be analyzed efficiently even when only modest computa...2493 days ago
Sequence - Evolution - Function; Computational Approaches in Comparative Genomics
Sequence - Evolution - Function is an introduction to the computational approaches that play a critic...role in the emerging new branch of biology known as functional genomics. The b...of the potential and limitations of computational and experimental approa...2481 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequ...tic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-...igh-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb....2367 days ago
Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave the course empowered to conduct independent genomic analyses. We will study the leading computa...2366 days ago
2366 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 elements for commonly...2365 days ago
Protein Subcellular Localization Prediction
Assigning subcellular localization to a protein is an important step towards elucidating its interaction partners, function, and potential role(s) in the cellular machinery. Computa...2274 days ago
Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but s...2262 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to join...repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into...2253 days ago