NEWS

clusnalyst 0.1.0

First release of the rewritten Clusnalyst, as an R package with the app inside.

Reads 0/1 band tables, SNP genotypes as letters, 0/1/2, VCF or HapMap, measured and categorical traits, and DNA or protein FASTA. The data type and table layout are detected and can be overridden.
Quality check step with filters for missing data, minor allele frequency and markers that do not vary. Sequences are aligned with ClustalOmega, ClustalW or MUSCLE.
New distances: allele sharing (IBS), modified Rogers, Euclidean, Manhattan, Gower, and K80, JC69, TN93 and p-distance for sequences.
New tree methods: WPGMA, Ward, BIONJ, and NJ rooted on an outgroup. A cophenetic correlation table compares them.
Number of groups from silhouette width, the within-group sum of squares and the gap statistic. Mantel tests against a second matrix or against numeric sample information such as location.
PCoA and PCA, and groups from cutting the tree, PAM or k-means.
Interactive trees and plots, sample information on hover, light and dark themes, a guided tour.
Downloads: PNG, SVG and PDF for every figure, CSV and Excel tables, Newick trees, an HTML report, an R script that repeats the analysis, and a session file.

The "Single" and "Complete" options ran Ward.D and Ward.D2.
Bootstrap support came from resampling the columns of the distance matrix. It now resamples markers (or alignment sites) and rebuilds the distances, as in Felsenstein (1985).
Data were kept in global variables, so people using the hosted app at the same time could overwrite each other's results. Each session now has its own state.
Choosing "already aligned" for a FASTA file crashed, and DNA could not be read.
Removing monomorphic markers failed when there were none, and letter genotypes with missing calls were coded wrongly.
Silhouette analysis failed for neighbour-joining trees.