Stars
The new Windows Terminal and the original Windows console host, all in the same place!
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Accelerated BLAST compatible local sequence aligner.
The second version of the Kraken taxonomic sequence classification system
Bayesian haplotype-based genetic polymorphism discovery and genotyping.
a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
Fast genome and metagenome distance estimation using MinHash
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
IQ-TREE software version 2: phylogenetics by maximum likelihood
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which wil…
[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)
De novo genome assembler for long uncorrected reads
Efficient phylogenomic software by maximum likelihood
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output inc…
ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
A whole-genome and alignment-free prokaryotic phylogeny tool
Program for finding horizontal gene transfer using BLAST result