Changes in version 0.1.0                        

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

Compared with the 2022 app

  - 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.

Fixed from the 2022 app

  - 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.