Processes Binary Data Obtained from Fragment Analysis (Such as AFLPs, ISSRs, and RFLPs)
Checks binary matrix for unwanted characters.
Consolidates replicate pairs in a binary matrix.
Calculates Jaccard and Euclidean error rates.
Outputs group names specified in the input file for the creation of an...
Creates a non-metric multidimensional scaling plot (nMDS).
Removes samples with peaks equal to or less than a specified threshold...
Calculates peak numbers for a consolidated data set (total, maximum, a...
Calculates peak numbers for the data set with all replicates (total, m...
Draws a scree plot.
Creates a shepard plot.
Draws a hierarchical clustering tree (UPGMA).
A molecular genetics tool that processes binary data from fragment analysis. It consolidates replicate sample pairs, outputs summary statistics, and produces hierarchical clustering trees and nMDS plots. This package was developed from the publication available here: <https://www.sciencedirect.com/science/article/pii/S1049964420306538>. The GUI version of this package is available on the R Shiny online server at: <https://clarkevansteenderen.shinyapps.io/BINMAT/> or it is accessible via GitHub by typing: shiny::runGitHub("BinMat", "clarkevansteenderen") into the console in R. Two real-world datasets accompany the package: an AFLP dataset of Bunias orientalis samples from Tewes et. al. (2017) <https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2745.12869>, and an ISSR dataset of Nymphaea specimens from Reid et. al. (2021) <https://www.sciencedirect.com/science/article/pii/S0304377021000218> . The authors of these publications are thanked for allowing the use of their data.