Main steps for phylogenetic reconstruction

1. Select your species. (<– the most important step!)
2. Align sequences.
3. Remove irrelevant or positions/columns that add noise.
4. Run phylogenetic inference.
5. Understand your phylogenetic tree. (<– the most important step!)
6. Come back to step 1, if needed.

The most important steps of phylogenetic inference are the species selection and the interpretation of your resulting tree. Yet, to be able to fully understand a phylogenetic tree, you need to understand how to build it. Here we will quickly go through every step. Yet keep in mind that each tree is a hypothesis of your given data, and therefore the selection of your species, the phylogenetic inference and the interpretation of the tree will highly rely on your scientific question.

Basic pipeline

Please, bear in mind that there are many different ways to infer phylogenetic patterns among genes, proteins or even morphological characters (or other traits). Here I will just guide you through a basic step-by-step pipeline that I normally use for quick and exploratory analyses of DNA sequences.

First we set the variable name of our input fasta file as follows:

FASTA="file.fasta"  # The raw fasta file

# And we call the output files as follows:
ALIGNED=${FASTA/.fasta/_align.fasta}  # The aligned fasta file
FILE=${ALIGNED/.fasta/_trimed.fasta}  # The aligned and trimmed fasta file ready for phylogenetic inference
OUTPUT="test1"  # The tree name prefix