ReOrderAlignment: Re-order sequences based on starting position

In coleoguy/evobir: Evolutionary Biology in R

Re-order sequences based on starting position

Description

This function re-orders aligned sequences with sequences based on the site of the alignment that they first have data. It also allows user to select reference sequences that will stay at the top of the alignmment regardless of starting position.

Usage

ReOrderAlignment(file, newfile, ref = "")

Arguments

file	the name of the fasta file which has sequences need to be re-ordered
newfile	name of the output file
ref	Either an integer or a characrter vector. Elements of the vector should match the sequences that should be kept at the top of the alignment.

Value

A fasta file

Author(s)

Sean Chien and Heath Blackmon

References

http://coleoguy.github.io/

coleoguy/evobir documentation built on July 27, 2023, 12:40 p.m.