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Changelog

Source: NEWS.md

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 , 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 (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

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

GenomAutomorphism 0.99.0