simuG: a general-purpose genome simulator
Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweig...1682 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 used...1672 days ago
HaploTypo: a variant-calling pipeline for phased genomes
An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most genetic variant calling tools do not explicitly account for ha...1661 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal...1645 days ago
NextDenovo: string graph-based de novo assembler for TGS long reads
NextDenovo is a string graph-based de novo assembler for TGS long reads. It uses a "correct-then-assemble" strategy similar to canu, but requires significantly le...1644 days ago
heatmaply: popular graphical method for visualizing high-dimensional data
This work is based on ggplot2 and plotly.js engine. It produces similar heatmaps as d3heatmap, with the advantage of speed (plotly.js is able to handle larger size matrix),...1638 days ago
1635 days ago
MGSE: Mapping-based Genome Size Estimation
MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly an...1632 days ago
1628 days ago
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assemb...1625 days ago