# 16.7: Sequence Alignment and Tree Building

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## 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

 1 2 3 4 5 6 7 8 9 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