UGENE
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:
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unzip orange.zip
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
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