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 a...2542 days ago
Sequence - Evolution - Function; Computational Approaches in Comparative Genomics
Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology...2523 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wiki...ryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s1305...put paired-end sequences. Journal of Computational Biology,...2410 days ago
2408 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 u...2408 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
PLAST is a fast, accurate and NGS scalable bank-to-bank se...takes full advantage of recent multi-core personal computers without requiring any additi...small RAM footprint, Ready to be used on desktop computer, cluster, cloud as well as wi...2406 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 a...2304 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into...repeats. The previous standard for evaluation (Hunt et al., Genome Biology,...2295 days ago
BEAP: Blast Extension and Assembly Program
The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide da...2214 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for singl...or effectively de novo assemblying large genomes. For example, on a 32-thread computer with 2.0 GHz CPU , MECAT take...2245 days ago