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A guide to using the R package 'ape' to reorder Newick trees, ensuring specific samples are placed as closely as possible without disrupting the tree hierarchy.
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How to Reorder Newick Trees for Optimal Sample Proximity

Introduction

If you're working with phylogenetic trees, you may encounter situations where you want specific samples to be positioned as close to each other as possible. This requirement often arises in studies where you are analyzing relationships among different species or samples based on genetic information.

In this guide, we will explore how to achieve this goal using an example Newick tree and the rotateConstr function from the R package ape. We’ll break down the problem, the solution, and provide examples to illustrate the process effectively.

The Problem

You might have a Newick tree like this:

[[See Video to Reveal this Text or Code Snippet]]

Your task is to position two chosen samples (from a, b, c, or d) as close to each other as possible without disrupting the lineage of the tree. For instance, if you want to place samples b and d together, you would want the output to resemble:

[[See Video to Reveal this Text or Code Snippet]]

This task can get more complicated with larger trees. For example:

[[See Video to Reveal this Text or Code Snippet]]

If you want to position b and f close together, you expect a rearrangement that may look like this:

[[See Video to Reveal this Text or Code Snippet]]

This is where the rotateConstr function comes into play.

The Solution: Using rotateConstr

The rotateConstr function is available in the ape R package and is specifically designed to help rearrange tree structures while respecting certain constraints.

Steps to Use rotateConstr

Install and Load the ape Package: If you haven’t installed the ape package yet, you can do so by running the following command in R:

[[See Video to Reveal this Text or Code Snippet]]

Once installed, load the package:

[[See Video to Reveal this Text or Code Snippet]]

Define Your Newick Tree: You can enter your Newick tree using the read.tree function.

[[See Video to Reveal this Text or Code Snippet]]

Apply rotateConstr for Specific Samples: Now, to position your desired samples close together, you will use the rotateConstr function. Here’s how you can do it:

For samples b and f:

[[See Video to Reveal this Text or Code Snippet]]

Optimal Rearrangement with Full Constraints: Although the function can work with partial constraints, it performs better with a complete list of ordered tip labels:

[[See Video to Reveal this Text or Code Snippet]]

This ensures that the tree maintains its structure while bringing your chosen samples together effectively.

Conclusion

Reordering Newick trees for specific samples to be positioned closely is a useful technique in phylogenetic analysis. By utilizing the rotateConstr function from the ape package in R, you can achieve this without disrupting the lineage of the tree.

Experiment with different configurations and options to better understand how your data can be represented. This method exemplifies the flexibility and power of R in managing complex biological data structures.

If you face any issues or have further questions, don’t hesitate to reach out or leave a comment below!