get.tree.seqs: Determine Tree Consensus Sequences

In matdoering/openPrimeR: Multiplex PCR Primer Design and Analysis

Determine Tree Consensus Sequences

Description

Creates all possible consensus sequences from a phylogenetic tree.

Usage

get.tree.seqs(tree, max.degen, primer.candidates)

Arguments

tree	The phylogenetic tree.
max.degen	The maximal degeneration of consensus primers.
primer.candidates	Alignment of primers.

Details

Ambiguous sequences are only generated with a degeneracy of at most max.degen. The tree is iterated from leaves to the top, i.e., starting from least degeneracy to most degeneracy. Merges only take place when the degeneracy of the resulting sequence would be at most max.degen. Gaps are removed from the alignments.

Value

Data frame with consensus primers extracted from the tree.

matdoering/openPrimeR documentation built on July 4, 2025, 3:59 a.m.