836 days ago
Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
...disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obs...814 days ago
Ten quick tips for deep learning in biology
By taking a comprehensive and careful approach to deep learning based on critical thinking about research questions, planning to maintain rigor, and discerning how work might have far-...786 days ago
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the Cro...724 days ago
108 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
...P, many additional ortholog alignments can be generated from multi-copy gene families. For phylogenetic inference, users can choose a supermatrix approach and/or gene tree inference fo...88 days ago
ExRec: Exclusion of Recombined DNA
...o output the longest non-recombined sequence blocks from loci (current best practice) or randomly select non-recombined blocks from loci (a newer approach). Two other applications in t...53 days ago
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables...41 days ago
ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
ContigExtender, was developed to extend contigs, complementing de novo assembly. ContigExtender employs a novel recursive Overlap Layout Candidates (r-OLC) strategy that...11 days ago