Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing.Source text:(Orlando., 2015) Reconstructing ancient genomes and…
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SNPest
Desktop

SNPest

Models the genotyping and SNP calling from the raw read sequences in a fully…

Models the genotyping and SNP calling from the raw read sequences in a fully probabilistic framework. There are many advantages in using a probabilistic model: The sampling and sequencing process is…

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Anfo
Desktop

Anfo

A mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more…

A mapper in the spirit of Soap/Maq/Bowtie, but its implementation takes more after BLAST/BLAT. Anfo is most useful for the alignment of sequencing reads where the DNA sequence is somehow modified…

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MIA
Desktop

MIA Mapping Iterative Assembler

The basic idea of this program is to align DNA sequencing fragments (shotgun or…

The basic idea of this program is to align DNA sequencing fragments (shotgun or targeted resequencing) to a reference, then call a consensus. Then the consensus is used as new reference and the…

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mapDamage
Desktop

mapDamage

Computes nucleotide misincorporation and fragmentation patterns using…

Computes nucleotide misincorporation and fragmentation patterns using next-generation sequencing reads mapped against a reference genome. mapDamage 2.0 that extends the original features of mapDamage…

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PALEOMIX
Desktop

PALEOMIX

A flexible and user-friendly pipeline applicable to both modern and ancient…

A flexible and user-friendly pipeline applicable to both modern and ancient genomes, which largely automates the in silico analyses behind whole-genome resequencing. PALEOMIX is compatible with a…

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epiPALEOMIX
Desktop

epiPALEOMIX

Identifies epigenetic signatures in archaeological material from…

Identifies epigenetic signatures in archaeological material from high-throughput DNA sequencing data. epiPALEOMIX leverages on natural degradation processes that affect DNA after death and, thus,…

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ATLAS
Desktop

ATLAS Analysis Tools for Low-depth and Ancient Samples

Analyzes ancient samples that properly account for post-mortem damage (PMD).…

Analyzes ancient samples that properly account for post-mortem damage (PMD). ATLAS works directly from raw BAM files and contains all necessary methods to infer patterns of PMD, recalibrate base…

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schmutzi
Desktop

schmutzi

An iterative approach to jointly estimate present-day human contamination in…

An iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and…

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Gargammel
Desktop

Gargammel

A set of programs aimed at simulating ancient DNA fragments. Gargamel can…

A set of programs aimed at simulating ancient DNA fragments. Gargamel can simulate most common features of a DNA sequences, including post-mortem DNA damage and base misincorporations. It simulates…

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Odintifier
Desktop

Odintifier

A method for identifying insertions of organellar origin from modern and…

A method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. Odintifier represents the first integration of phasing…

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BWA-PSSM
Desktop

BWA-PSSM

A probabilistic short read aligner based on the use of position specific…

A probabilistic short read aligner based on the use of position specific scoring matrices (PSSM). Like many of the existing aligners it is fast and sensitive. Unlike most other aligners, however, it…

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leeHom
Desktop

leeHom

Removes the adaptors and reconstructs the original DNA sequences using a…

Removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. leeHom is faster, and provides a more accurate reconstruction of the…

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PMDtools
Desktop

PMDtools

A framework for evaluating the likelihood of a sequence originating from a…

A framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation-summarized in a postmortem degradation score-which allows the identification of DNA…

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