A phylogenetic tree is a hypothesis of the evolutionary inheritance of genes across individual taxa. Trees have been used to summarize an organism’s pedigree, infer viral host-spillover events (Zhou et al., 2020), and determine if the red panda is a bear or a raccoon (Slattery & O’Brien, 1995)

There are a number of phylogenetic tree building programs including BEAST, MrBayes, PAUP, PhyML, RAxML, IQ-Tree, and FastTree. We are focusing on FastTree because it tends to be a faster tree building program to provide a quick draft tree. We recommend running FastTree to get a general sense of individuals in the tree, subsample down or add references taxa to create a well formed tree, and then move on to the other tree-building programs for more detailed diversity and time-scaled analysis.

Software required

  • MAFFT - for aligning your sequences
  • FastTree - for building a quick phylogenetic tree from aligned sequences
    curl -O
    gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm
  • FigTree - for viewing your phylogenetic tree

Overview of the pipeline:

  sequences -> MAFFT -> FastTree -> FigTree -> pdf figure that can go into your manuscript

Step 1: MAFFT

mafft --auto input.fasta > input_aln.fasta

Step 2: FastTree

# For a nucleotide alignment
FastTree -nt -gtr -gamma input_aln.fasta > input.tre

# For a protein alignment
FastTree input_aln.fasta > input.tre

Step 3: FigTree

Open FigTree application and use File/Open Tree to select your input.tre. Usually the tree will be hard to read until you midpoint using the command keys Ctrl-M and Ctrl-U.