SOFTWARE & TOOLS
DORA
DORA (Data Overlays for Research in Archaeogenomics) is an interactive map that combines ancient DNA sample data with associated datasets, including ancient climatic conditions, population structure results, and polygenic scores. Additional layers can be added by users, such as additional samples or imputed genotypes. DORA can be used to run a variety of genetic analyses on ancient DNA, using the interactive interface, to demarcate samples according to their temporal and spatial positions.
Details in: Harris KD, Greenbaum G (2024). DORA: an interactive map for the visualization and analysis of ancient human DNA and associated data. Nucleic Acid Research, 52, W54-W80
NetStruct Hierarchy
NetStruct Hierarchy is a network-based method for inference of multiple hierarchical levels of population structure. The structure is summarized as a population structure tree (PST). An additional tool is available for visualizing the data and plotting it on geographic maps.
modelRxiv
modelRxiv is a web-based repository and platform for models in ecology and evolution. It allows researchers to upload and share published and unpublished models developed in different programming languages (currently supports Python, JavaScript and R). Anyone can then easily run, reparametrize, and visualize model results. The goal of modelRxiv is to facilitate review, dissemination, replication, and investigation of results from models in the ecology and evolution scientific community.
NetStruct
This is the original version of NetStruct, and is a network-based inference of population structure from genetic data. It is similar to NetStruct Hierarchy, but does not automatically infers hierarchical levels. Requires the software Mathematica software, and is implemented with a simple GUI.
