FastTree

Software required

  • MAFFT - for aligning your sequences
  • FastTree - for building a quick phylogenetic tree from aligned sequences
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    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:

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

Step 1: MAFFT

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mafft --auto input.fasta > input_aln.fasta

Step 2: FastTree

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# 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.

Citations