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16: Bioinformatics
16.7: Sequence Alignment and Tree Building

16.7: Sequence Alignment and Tree Building

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Page ID: 24921

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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

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

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