promotor_divergence_estimation: Estimate the DNA distance between promotor sequences

In HajkD/orthologr: Comparative Genomics with R

Estimate the DNA distance between promotor sequences

Description

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

Usage

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(s)

Hajk-Georg Drost

HajkD/orthologr documentation built on Oct. 13, 2023, 12:11 a.m.