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.
- MAFFT - for aligning your sequences
- FastTree - for building a quick phylogenetic tree from aligned sequences
curl -O http://www.microbesonline.org/fasttree/FastTree.c gcc -O3 -finline-functions -funroll-loops -Wall -o FastTree FastTree.c -lm
- FigTree - for viewing your phylogenetic tree
Overview of the pipeline:
1 sequences -> MAFFT -> FastTree -> FigTree -> pdf figure that can go into your manuscript
Step 1: MAFFT
1 mafft --auto input.fasta > input_aln.fasta
Step 2: FastTree
1 2 3 4 5 # 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
- Katoh, K., Misawa, K., Kuma, K.I. and Miyata, T., 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research, 30(14), pp.3059-3066.
- Price, M.N., Dehal, P.S. and Arkin, A.P., 2009. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular biology and evolution, 26(7), pp.1641-1650.
- Rambaut, A., 2007. FigTree, a graphical viewer of phylogenetic trees.