Compute promotor sequence divergence of orthologous genes

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.

Usage

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