filter_quality0: Selects a background reference set of sequences with good...

In emvolz-phylodynamics/sarscov2Rutils: Scripts to support preparation and analysis of SARS CoV 2 analyses

Description

- bat/pangolin/canine - sequences with many gaps - sequences within incomplete dates - sequences with poor relationship with a molecular clock

Usage

filter_quality0(
  path_to_align,
  path_to_save = NULL,
  q_threshold = 0.05,
  minEdge = 1/29000/10,
  deduplicate_identical = TRUE,
  ...
)

Arguments

path_to_save	Where to store (as fasta) the filtered alignment
q_threshold	Clock outlier threshold
minEdge	minimum branch length (substitutions per site) to stabilize clock inference
deduplicate_identical	if TRUE, will only include one sequence (most recent) from among sets of identical sequences

Value

Writes a new fasta aligment. Return value is a treedater tree and dnabin

emvolz-phylodynamics/sarscov2Rutils documentation built on Nov. 17, 2020, 9:22 a.m.