Changes in version 1.3.5                        

NEW FEATURES

  - Added function run_last() to run alternative BLAST search. Vignette
    was updated accordingly.

                        Changes in version 1.3.4                        

BUG FIXES

                        Changes in version 1.3.3                        

                        Changes in version 1.3.2                        

BUG FIXES

  - Strand information is now preserved in the output of process_input()
    (for users who want to plot synteny).

                        Changes in version 1.3.1                        

NEW FEATURES

  - Added function collapse_protein_ids() to replace protein IDs in
    sequence names (equivalent to FASTA headers) with gene IDs. If there
    are multiple protein for the same gene, onlt the longest is kept.
    Vignette was updated accordingly.

                        Changes in version 1.1.6                        

BUG FIXES

  - Added a check for which IQ-TREE version is installed. If IQ-TREE2 is
    installed (and not IQ-TREE), arguments and call are modified
    accordingly, because IQ-TREE developers changed some parameters
    (e.g., -bb is now -B).

NEW FEATURES

  - Added a parameter as to parse_collinearity() that allows the
    extraction on synteny block information from .collinearity files.
    The vignette was updated accordingly.

                        Changes in version 1.1.5                        

BUG FIXES

  - Fixed species ID retrieval by adding an exported function named
    create_species_id_table() that correctly creates unique species IDs
    (3-5 characters), even when the first 5 characters are equal.

  - intraspecies_synteny() and interspecies_synteny() (originally
    unexported) now take the same output of process_input(), which makes
    them consistent with the entire package.

NEW FEATURES

  - To make it easier for users who want to run DIAMOND from the command
    line, I added the functions export_sequences() and read_diamond(),
    which write processed sequences to FASTA files and read the DIAMOND
    output, respectively. An example code on how to run DIAMOND from the
    command line has been added to the vignette.

  - Included a section in the vignette on how to use syntenet as a
    synteny detection program (i.e., to find synteny within a single
    genome or between two genomes).

                        Changes in version 1.1.4                        

BUG FIXES

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

UPDATES

  - Added CITATION file with reference to published paper

                        Changes in version 1.1.3                        

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 1.1.2                        

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 1.1.1                        

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.