ClonalFrameML is a a software package that performs efficient inference of recombination in bacterial genomes.

Clustal Omega: the last alignment program you'll ever need.

CNVpytor is a Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads developed in Abyzov Lab, Mayo Clinic.

CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species.

Corona Lite is a genome alignment tool.

Cufflinks is a reference-guided assembler for RNA-Seq experiments. It simultaneously assembles transcripts from reads and estimates their relative abundances, without using a reference annotation.

dDocent was designed as a scripted software pipeline made for analyzing double digest RAD (Peterson et al. 2012) or ezRAD (Toonen et al. 2013) data in highly polymorphic marine species.

deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.