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