Estimate the DNA distance between promotor sequences

Source: R/promotor_divergence_estimation.R

Given two fasta files storing the promotor sequence of protein coding genes, this function estimates the pairwise DNA distance between these promotor sequences.

promotor_divergence_estimation(query, subject, model = "K80")

Arguments

query

file path to a query fasta file storing promotor sequences of interest (e.g. generated with extract_upstream_promotor_seqs).

subject

file path to a subject fasta file storing promotor sequences of interest (e.g. generated with extract_upstream_promotor_seqs).

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

Author

Hajk-Georg Drost