Computational Tools and Analysis Section

Overview

This section provides an indexed list of computational methods, software packages, scripts, and analytical tools utilised within bioarchaeological research as described in the Manual. Each listed tool includes a concise description, intended application, and links to relevant webpages and GitHub repositories, including specific guidance on usage, robustness, error analysis, and reliability criteria.

Tools by Application

Proteomics

• MaxQuant

  • Description: Comprehensive quantitative proteomics software suite designed for analysing large mass-spectrometry data.

  • Webpage: MaxQuant

  • Repository: GitHub/MqTools7

  • License: Freeware (proprietary but freely available)

  • Reliability Criteria: Robust peptide identification with built-in false discovery rate (FDR) assessment.

• MetaMorpheus

  • Description: Software for high-throughput proteomics with enhanced sensitivity and comprehensive search capabilities.

  • Webpage: MetaMorpheus

  • Repository: GitHub/MetaMorpheus

  • License: Open-source (MIT License)

  • Documentation: 

• Spectronaut

  • License: Proprietary (commercial license)

  • Website: biognosys.com/software/spectronaut

  • Documentation

• Scaffold

  • License: Proprietary (per device license)

  • Website: proteomesoftware.com

  • Documentation

• Comet

  • License: Open-source (Apache License 2.0)

  • Website: https://uwpr.github.io/Comet/

• SPIN (Species by Proteome INvestigation) workflow

  • Reference: https://www.nature.com/articles/s41467-022-30097-x

  • Documentation

Lipid Analysis

• MassHunter

  • Description: Software for acquiring and processing mass spectrometry data, tailored especially for gas chromatography (GC-MS, GC-FID).

  • Webpage: MassHunter Software

  • Documentation

• Omnic

  • Description: Software suite for Fourier-transform infrared (FTIR) spectroscopy that can be used for lipid analysis and interpretation.

  • Webpage: ThermoFisher Scientific - Omnic

  • Documentation:

• LipidSearch

  • License: Proprietary (free 60-day trial available)

  • Website: thermofisher.comthermofisher.com

• LipidFinder

  • License: Open-source (MIT License)

  • GitHub: ODonnell-Lipidomics/LipidFinderlifs-tools.org

• LIQUID

  • License: Open-source (Apache License 2.0)

  • Website: data.pnnl.gov

• LipidOne 2.0

  • License: Freeware (usage terms not specified)

  • Website: lipidone.eu

• Lipidome Projector

  • License: Open-source (MIT License)

  • Website: lifs-tools.org

• LipidSig

  • License: Open-source (Creative Commons BY-NC 4.0)

  • Website: lipidsig.bioinfomics.orgacademic.oup.com

Microfossil Analysis

• FossilMorph

  • License: Open-access (specific license not specified)

  • Reference: ScienceDirect Article

• 3DHISTECH

  • License: Proprietary (commercial license)

  • Website: 3dhistech.com

Radiocarbon Dating

• OxCal

  • Description: Calibration software for radiocarbon dating, widely used for converting radiocarbon years (BP) to calendar dates.

  • Webpage: OxCal Calibration Software

  • Documentation: Detailed workflows available in OxCal Online Manual

  • License: Freeware (free to use and distribute)

• rcarbon (R package)

  • Description: An R package for calibration and statistical analysis of radiocarbon dates.

  • License: Open-source

  • Repository: GitHub/rcarbon

  • Instructions: Package documentation available online; supports reproducible data analysis workflows.

• BCal

  • License: Freeware (usage terms not specified)

  • Website: bcal.shef.ac.uk

• CALIB

  • License: Freeware (usage terms not specified)

  • Website: calib.org

Stable Isotope Analysis

• IsoReader

  • Description: Software for standardized reading, processing, and managing stable isotope data.

  • Repository: GitHub/IsoReader

  • License: Open-source (MIT License)

• MixSIAR

  • Description: Bayesian mixing model designed to analyze stable isotope data, useful for diet reconstruction studies.

  • Repository: GitHub/MixSIAR

  • License: Open-source (license not specified)

• Escher-Trace

  • License: Open-source (license not specified)

  • Website: escher-trace.github.io

• IsoSource

  • License: Freeware (usage terms not specified)

  • Reference: EPA Resourcelipidsig.bioinfomics.org+2BioMed Central+2Comet+2

• IsoError

  • License: Freeware (usage terms not specified)

  • Reference: EPA Resource

ZooMS Analysis

• mMass

  • Description: Open-source mass spectrometry software for ZooMS data analysis.

  • Webpage: mMass

  • Repository: GitHub/mMass

  • Instructions: Protocols.io guide available here.

• PAMPA

  • License: Not specified; likely open-access for academic use

  • Reference: bioRxiv Article3DHISTECH+1lifs-tools.org+1

• SpecieScan

  • License: ?

  • Reference: Bioinformatics Articleproteomesoftware.com

General Guidelines for Computational Tools

• GitHub Repositories:

  • Scripts used in data processing and analysis are archived and publicly accessible via GitHub. Repository details include commit histories and version control for reproducibility.

• R scripts

• Instructions for Usage:

  • Each computational tool comes with clearly documented instructions. Usage protocols include required data formats, step-by-step execution guidance, and troubleshooting sections.

• Robustness and Error Analysis:

  • Analytical scripts and software provide error handling and robustness checks, including internal quality controls, validation datasets, and repeat analyses for accuracy verification.

• Reliability Criteria:

  • Tools have been selected based on peer-reviewed reliability, robustness of results, reproducibility, and community endorsement within bioarchaeological research contexts.

This structured documentation supports the consistent use and rigorous application of computational methodologies within bioarchaeological investigations, fostering transparent and reproducible research practices.