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...2364 days ago
2336 days ago
snakepipes: A toolkit based on snakemake and python for analysis of NGS data
snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data. DNA-mapping* ChIP-seq* RNA-seq* ATAC-seq* scRNA-seq...1817 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...2272 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined usin...paring human GENCODE genes (from GENCODE v30) to lncRNAs from other species identifie...Assembly Code Transcriptome lncRNAs...864 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...2260 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers...me repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into...2251 days ago
SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences with focus on health and en...ly 2016 November - Uppsala2017 November - Uppsala RNA-seq course 2015 October - Up...- Uppsala2017 March - Uppsala2017 November - UppsalaRNAseq...2225 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcri...2204 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to...2204 days ago