Compute promotor sequence divergence of orthologous genes

Source: R/promotor_divergence_of_orthologous_genes.R

This function computes the promotor sequence divergences of orthologous genes from a set of pairwise species comparisons. It allows to add this promotor divergence information to an pre-computed dNdS table generated with dNdS or generate_ortholog_tables_all.

promotor_divergence_of_orthologous_genes(
  promotor_folder,
  ortholog_tables_folder,
  model = "K80",
  ortholog_promotor_seq_output = NULL
)

Arguments

promotor_folder

a path to a folder containing promotor sequences in fasta format that were generated with extract_upstream_promotor_seqs.

ortholog_tables_folder

a path to a folder containing dNdS tables generated with generate_ortholog_tables_all

model

a model as specified in dist.dna: a character string specifying the evolutionary model to be used - must be one of:

  • K80 (the default)

  • raw

  • N

  • TS

  • TV

  • JC69

  • F81

  • K81

  • F84

  • BH87

  • T92

  • TN93

  • GG95

  • logdet

  • paralin

ortholog_promotor_seq_output

a path or name to an output folder where orthologous promotor sequences shall be stored.

Author

Hajk-Georg Drost