NEWS

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GenomAutomorphism 1.15.2

• Fix Bioconductor devel build failure from Biostrings >= 2.81.3 (Bioconductor 3.24). Adapt to Biostrings >= 2.81.3 (Bioconductor 3.24), where DNAMultipleAlignment, AAMultipleAlignment, and readDNAMultipleAlignment moved to the new MultipleAlignment package. Import from MultipleAlignment, declare the S4 class via importClassesFrom(), add explicit DNAMultipleAlignment methods, and regenerate bundled MSA datasets. This fixes lazy-loading and example failures on the Bioconductor build system. (Not applicable to Bioconductor 3.23 / Biostrings 2.80.1.)

GenomAutomorphism 1.15.1

• Update math documentation notation and BiocCheck vignette fixes

GenomAutomorphism 1.15.0

• Fix a bug in the internal function 'weighted_manhattan' (used by 'codon_dist', 'codon_dist_matrix', and 'aminoacid_dist') where, for \eqn{group = "Z4"}, the second coordinate weight ('w[2]') was silently omitted and 'w[3]' was applied twice instead, contradicting the documented weighted Manhattan distance formula. This changes the numeric distances returned for \emph{group = "Z4"} (the default). The bundled 'cdm_z64' dataset was regenerated accordingly.

• Documentation updated

GenomAutomorphism 1.8.1

• Add new a new function: 'automorphism_prob', which applies a Dirichlet-Multinomial Modelling (in a Bayesian framework) to compute the posterior probability of each type of mutational event.

GenomAutomorphism 1.5.1

• Introducing new functions for DNA and aminoacid sequence representations with physicochemical properties of DNA and aminoacids, which would be useful for further downstream statistical analysis in R.

GenomAutomorphism 1.0.2

• Fix error of parallel computation on Windows (12/08/2022)

GenomAutomorphism 1.0.1

• Expanding analyses by including aminoacid similarity based on codon distances. Three new functions are added: codon_dist, codon_dist_matrix, and aminoacid_dist. See a tutorial applying these functions at https://is.gd/oYLDK4.

GenomAutomorphism 1.0.0

• Release in Bioconductor (version 3.16). https://doi.org/doi:10.18129/B9.bioc.GenomAutomorphism

GenomAutomorphism 0.99.4

• Expanding analyses by including amino acid similarity and statistical protein contact potentials matrices from from Amino Acid Index Database https://www.genome.jp/aaindex/.
• Improving documentation.
• Fixed a bug which introduced a change of protein coding frameshift.

GenomAutomorphism 0.99.3

• Documentation improvement.
• Package accepted on Bioconductor (07/18/22)

GenomAutomorphism 0.99.2

• Updating several details after the review process in Bioconductor (https://github.com/Bioconductor/Contributions/issues/2678)

GenomAutomorphism 0.99.0

• Available at https://github.com/genomaths/GenomAutomorphism
• Release: February 28, 2022
  • Initial development.