RNA-seq aligner

De novo assembler for single molecule sequencing reads using repeat graphs

HMMER: biological sequence analysis using profile HMMs

Align proteins to genomes with splicing and frameshift

Inference of ploidy and heterozygosity structure using whole genome sequencing data

haplotypic duplication identification tool

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

Evaluate variant calls and its combination with k-mer multiplicity

PoSeiDon: positive selection detection and recombination analysis pipeline

Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.

Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.

R Interface to CoreArray Genomic Data Structure (GDS) Files (Development version only)

Co-phylog: an assembly-free phylogenomic approach for closely related organisms