Archaeogenetics

adrsm

A tool designed to simulate the paired-end sequencing of a metagenomic community.

AncientMetagenomeDir

Repository containing lists of all published ancient metagenome samples (and related).

anfo

The ANFO ancient DNA mapper.

angsd

Program for analysing next generation sequencing data.

AntCaller

SNP calling and genotyping for damaged DNA.

archaeodiet

Pipeline for metagenomic identification and authentication of ancient dietary DNA from archaeological samples.

ARIADNA

Machine Learning Method for Ancient DNA Variant Discovery.

atlas

A set of tools that cover all programs necessary to obtain variant calls, estimates of heterozygosity and more from a BAM file.

AuthentiCT

Estimate the proportion of present-day DNA contamination in ancient DNA datasets generated from single-stranded libraries.

Consensify

Consensify method for error reduction in ancient DNA pseudohaploidisation.

ContamLD

Software designed to estimate autosomal contamination in ancient DNA samples.

coproID

CoproID helps you to identify the “true maker” of Illumina sequenced Coprolites/Paleofaeces by checking the microbiome composition and the endogenous DNA.

cuperdec

R package to generate ‘Cumulative Percent Decay’ curves, with optional filtering functions, for microbial taxonomic profiles.

DamageProfiler

A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage.

DamMet

A full probabilistic model for mapping ancient methylomes.

DATES

Method for dating admixture in ancient DNA specimens.

dice

Joint estimate of demography and contamination for nuclear ancient DNA.

eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline.

EAGER-CLI

A fully reproducible and state-of-the-art ancient DNA analysis pipeline.

EAGER-GUI

A fully reproducible and state-of-the-art ancient DNA analysis pipeline.

epiPALEOMIX

A fast, accurate, and automatic pipeline for generating nucleosome and methylation maps from high throughput sequencing data underlying ancient samples.

gargammel

A set of programs aimed at simulating ancient DNA fragments. For ancient hominin samples our program can also simulate various levels of present-day human contamination and microbial contamination.

hapROH

Software to call ROH from ancient and present-day DNA using reference haplotypes.

HOPS

A pipeline which focuses on screening MALT data for the presence of a user-specified list of target species.

leeHom

Bayesian reconstruction of ancient DNA fragments.

MADAM

Two-level de novo assembly strategy for ancient bacterial genomes.

MALT

A sequence alignment and analysis tool designedfor processing high-throughput sequencing data, especially in the context of metagenomics.

mapDamage

Tracking and quantifying damage patterns in ancient DNA sequences.

mapping-iterative-assembler

Consensus calling (or “reference assisted assembly”), chiefly of ancient mitochondria.

maximum-likelihood-relatedness-estimation

Infer biological relatedness from low coverage 2nd generation sequencing data.

metabit

An integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data.

MultiVCFAnalyzer

A SNP filtering and SNP alignment generation tool, designed around (but not limited to) low coverage ancient DNA data.

paleomix

Pipelines and tools for the processing of ancient and modern High-Throughput Sequencing (HTS) data.

pathPhynder

A workflow for integrating ancient lineages into present-day phylogenies.

pileupcaller

Sample alleles from low coverage sequence data.

PMDtools

Compute postmortem damage patterns and decontaminate ancient genomes.

poseidon-framework

Poseidon is a framework that seeks to provide standardized ways to store and share archaeogenetic, and perhaps more broadly, molecular archaeological datasets.

READ

A method to infer the degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for a pair of low-coverage individuals.

schmutzi

Maximum a posteriori estimate of contamination for ancient samples.

Sex.DetERRmine

Calculate the relative coverage of X and Y chromosomes, and their associated error bars, from the depth of coverage at specified SNPs.

snpAD

Implements an iterative method to jointly estimate error rates and genotypes frequencies from the data.

SPARSE

Indexes >100,000 reference genomes in public databases in to hierarchical clusters and uses it to predict origins of metagenomic reads.

statuAAR

Estimation of human stature from long bone measurements according to several well established estimation formula.

tapas

Evaluate the effectiveness of any short read mapper and its parameters using artificially generated reads.

TOPAS

A toolkit for efficient manipulation of sequence data in various ways.

yada

yada, which stands for Yet Another Demographic Analysis package, supports a variety of demographic tasks, with most applications drawn from forensic anthroplogy and archaeology.