Phylogeny

How to Phylogeny (Part 2: Maximum Likelihood Tree Building)

Disclamer: I’m a trained microbiologist/biochemist, which means most of my bioinformatics knowledge was self-taught. What you’re about to see may not be pretty; the code might be janky or the workflow inefficient. But I have gone through countless hours of googleing, reading, and trial/error to learn this, and it works pretty well for me, so it might for you too. Let me know if you spot errors or have suggestions for improvement!

How to Phylogeny (Part 0: Getting and Cleaning Data)

1 Introduction 1.1 Essential Tools and Basic Knowledge 1.1.1 Fasta Format 1.1.2 Notepad++ 1.1.3 BioEdit 1.1.4 Unix Terminal 1.1.5 R 1.2 Getting Data 1.2.1 Keyword Search 1.2.2 BLAST 1.3 Cleaning Data 1.3.1 Concatenate Sequences 1.3.2 Remove Duplicate Sequences 1.3.3 Remove False Hits 1.3.4 Trim Extra Domains 1.3.5 Clean up Names 1.4 Conclusions Disclamer: I’m a trained microbiologist/biochemist, which means most of my bioinformatics knowledge was self-taught.

How to Phylogeny (Part 1: Sequence Alignment)

Disclamer: I’m a trained microbiologist/biochemist, which means most of my bioinformatics knowledge was self-taught. What you’re about to see may not be pretty; the code might be janky or the workflow inefficient. But I have gone through countless hours of googleing, reading, and trial/error to learn this, and it works pretty well for me, so it might for you too. Let me know if you spot errors or have suggestions for improvement!