Sequence Alignment and Tree Building


The following video illustrates the tree building process using MUSCLE and PhyML in UGENE.

Command Line

The following requires:

  • A UNIX-like environment like Linux or MacOS
  • MUSCLE to perform a multiple sequence alignment
  • PhyML to generate Maximum Likelihood
  • FigTree to manipulate the tree

Download the example file oranges. In the download directory, perform the following:

cd orange
cat ./*txt >> oranges.fasta  ## merges all files into a single fasta file
muscle -in oranges.fasta -phyiout oranges.phy
## -phyiout tells muscle to use the interleaved phylip format for output
phyml -i oranges.phy -m HKY85
## -m is for method and HKY85 is the default nucleotide method we used in UGENE
mv oranges.phy_phyml_tree.txt oranges.nwk
## change the name of the output to reflect it is a nwk file