Changes in version 1.0.4                        

BUG FIXES

  - Replaced sprintf calls with snprintf in C++ code to address warnings
    in the devel branch of Bioc

UPDATES

  - Added CITATION file with reference to published paper

                        Changes in version 1.0.3                        

BUG FIXES

  - Tidy evaluation with aes_() was deprecated in ggplot 3.0.0, and
    testthat now returns warnings for it. Replaced aes_() with aes() and
    .data from the rlang package.

                        Changes in version 1.0.2                        

NEW FEATURES

  - Added parameters clust_function and clust_params in
    cluster_network() to let users pass any igraph::cluster_* function
    to cluster the synteny network.

  - Added parameters clust_function and clust_params in plot_profiles()
    to let users have more control on the method used to cluster the
    distance matrix (columns in phylogenomic profiles).

  - Updated vignette to reflect the changes mentioned above and included
    an FAQ item with instructions on how to update the R PATH variable.

                        Changes in version 1.0.1                        

NEW FEATURES

  - Ward's clustering of synteny clusters is now performed prior to
    plotting in plot_profiles(), not in phylogenomic_profile(). As a
    consequence, phylogenomic_profile() now returns only a matrix of
    profiles, not a list containing the matrix and an hclust object.

  - Added an option to handle names in vector cluster_species as new
    names for display in the heatmap. This way, species abbreviations
    can be easily replaced with species' full names to make plots look
    better.

  - Added parameters dist_function and dist_params to allow users to
    specify function and parameters to calculate the distance matrix
    that will be passed to Ward's clustering.

                       Changes in version 0.99.7                        

NEW FEATURES

  - Added functions fasta2AAStringSetlist and gff2GRangesList to help
    users read multiple FASTA and GFF/GTF files as list of AAStringSet
    and GRangesList, respectively.

  - Updated vignette to instruct users on how to load FASTA and GFF/GTF
    files to the R session.

                       Changes in version 0.99.5                        

NEW FEATURES

  - Replaced distance measure for clustering of phylogenomic profiles:
    from vegan::vegdist to labdsv::dsvdis

                       Changes in version 0.99.0                        

NEW FEATURES

  - Added a NEWS.md file to track changes to the package.