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alib

arraydesign

bam2prof

the subprogram in schmutzi but rewritten using htslib

bamtools

C++ API & command-line toolkit for working with BAM data

baselengthfilter

This program reads a BAM and produces another with a length filter applied on reads

bcl2bam2fastq

bedbamandbeyond

betascan

Genome-wide scan for balancing selection using beta statistic

bibtexfixcaps

Fix the capitalization problems for bibtex.

bioconda-recipes

Conda recipes for the bioconda channel.

bowtie2

A fast and sensitive gapped read aligner

cinch

deml

Maximum likelihood demultiplexing

dice

Joint estimate of demography and contamination for nuclear ancient DNA

dist2nj

transform the distance output from glactools into a neighbor joining tree

dna2int

quick benchmarking to check the best way to transform DNA letters to integers

epoparser

This program an EPO alignment index and fasta index for the genome and produces a tab delimited output

fastautils

Little programs to handle fasta files

freeibis

An efficient basecaller for Illumina sequencers with calibrated quality scores

gargammel

gargammel is an ancient DNA simulator

genstat

glactools

command-line tools for the management of genotype likelihoods and allele counts

grenaud

grenaud.github.io

gross

Graph-aware Retrieval of Selective Sweeps

insertsize

Simple C++ program built using samtools to get the insert size from BAM files

isbarch.github.io

Website for the International Society for Biomolecular Archaeology

leehom

Bayesian reconstruction of ancient DNA fragments

libbam

Library of various programs based on bamtools

libgab

A C++ class of useful little functions