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MIA / Mapping Iterative Assembler
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 process is repeated until convergence. Since it was originally designed to be used on ancient DNA, it supports a position specific substitution matrix, which improves both alignment and consensus calling on chemically damaged aDNA. MIA has been used to assemble a number of Neandertal and early modern human mitochondria.
Gargammel
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 base compositional bias due to the molecular tools used in library preparation, sequencing bias against GC-rich fragments and errors introduced by the sequencing platform. Gargammel provides researchers with the opportunity to perform various inquiries to evaluate the robustness of various analyses to a DNA properties.
epiPALEOMIX
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, does not require prior treatment of ancient DNA extracts with gold-standard epigenetic methods, such as bisulfite or chip-seq. It can reveal genome-wide patterns of CpG methylation, and can generate nucleosome maps and phasogram analyses. epiPALEOMIX can accommodate any type of molecular tools used to prepare ancient DNA (aDNA), including USER-treatment of DNA extracts and amplification of DNA libraries with uracile-intolerant DNA polymerase, such as the Phusion DNA polymerase.
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