seq_designation: Sequence Lineage Designation

In KathrynCampbell/MADDOG: Lineage Designation and Assignment

Sequence Lineage Designation

Description

This function designates the lineages of a set of sequences given the tree, alignment, ancestral reconstructions and metadata of the sequences. The sequence IDs must match between all of these. The metadata file must have a column called 'ID' which contains the ID's for all the sequences. It also must have a column called 'year' that contains the collection year of each sequence. Additionally, it must have a column called 'country'. This should contain the country of origin of each sequence. If you don't have this information, you can leave the column blank but it needs to exist. If you have more detailed information about the origin of the sequence (e.g. a state) you can put this in the country column instead of the country. It also needs to have an 'assignment' column which contains any known clade assignments. If you don't have this information, you can leave this column blank but it needs to exist.

Usage

seq_designation(tree, min.support, alignment, metadata, ancestral)

Arguments

tree	A phylogenetic tree
min.support	The minimum bootstrap support required
alignment	The alignment in fasta format that corresponds to the tree
metadata	The metadata corresponding to the sequences in the tree, including "ID" "assignment" "country" and "year"
ancestral	The fasta file of the reconstructed ancestral sequences for the tree, generated by Treetime

Value

Information about the input sequences and their lineage designation

KathrynCampbell/MADDOG documentation built on April 14, 2025, 10:40 a.m.