This page provides an organized index of relevant tools, databases, and services used in bioarchaeological research, especially in the analysis of DNA, proteomics, isotopes, and other biochemical data. Each tool links to a dedicated page with more information.
| Tool | Description |
|---|
| MINAS | A community-driven specification for describing metagenomic and metatranscriptomic samples. Website |
| UNIPROT | A comprehensive resource for protein sequence and functional information, including SwissProt, TrEMBL, and associated annotation tools. |
| eHOMD | The expanded Human Oral Microbiome Database, useful for ancient oral microbiome studies. Link |
| CRAP Database | A database of common lab contaminants in proteomics workflows. Helpful for filtering out false positives. |
| Tool | Description |
|---|
| MaxQuant | A quantitative proteomics software package for mass spectrometry-based proteomics. Often paired with Andromeda search engine. |
| Novor Cloud | A fast, real-time de novo sequencing tool for peptides, available as a cloud service. |
| MSFragger | A mass spectrometry database search tool known for speed and open modification search capabilities. |
| pFind | A comprehensive database search engine for proteomics data. |
| Sage | Proteomics software for advanced search and post-processing, developed for large-scale data analysis. |
| mMass | Open-source software for annotation and interpretation of mass spectra. Link |
| MassHunter | Agilent's software suite for mass spectrometry data acquisition and analysis. |
| Tool | Description |
|---|
| IsoReader | An R package for importing and handling isotope ratio mass spectrometry data in structured workflows. Especially useful with continuous-flow IRMS. |
| mixSIAR | A Bayesian mixing model framework in R for estimating diet composition from stable isotope data. Flexible with covariates and hierarchical models. |
| IsotopeR | R-based tool for isotope data analysis, including quality checks, basic plotting, and statistical summaries. Good for quick explorations. |
| FRUITS | Food Reconstruction Using Isotopic Transferred Signals — a GUI-based Bayesian mixing model for dietary reconstruction with prior constraints. Link |
| Lyticos | A lesser-known tool aimed at visualizing and interpreting isotope data in archaeological contexts. Useful for exploring multi-isotope datasets. |
| Tool | Description |
|---|
|
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| OxCal | Widely used for Bayesian calibration of radiocarbon dates. Website |
| BCal | An on-line Bayesian radiocarbon calibration tool |
rcarbon | R package for the analysis of large collections of radiocarbon dates |
ChronoModel | An open-source application developed at CNRS: https://chronomodel.com/ |
| Tool | Description |
|---|
| R | Statistical computing environment. Widely used in isotope and DNA analysis pipelines. |
| Python | A flexible programming language with libraries for genomics, proteomics, and statistical analysis. |
| Tool | Description |
|---|
| Zenodo | Open-access repository for research data and software. Link |
| Dryad | Curated resource for data underlying scientific publications. Link |
| dataDOI | Estonian research data repository https://datadoi.ee/ |
| GitHub | Code hosting platform used for version control and software dissemination in academic bioinformatics. |