In today's lab we are going to build trees using the Distance Based, Neighbour Joining method and the character-based Maximum Parsimony.
In newick format you can also encode the length of the branches by including the branch length after a colon ":" like this exampl
round a new kind of object to represent a phylogenetic tree called a tree
we are more likely to read trees from a file
Again like SeqRecords or Alignments we can use read() from Phylo to read in a single tree:
The first is the name of an opened file object
The second argument is the format of tree file
he tree format newick is by far the most common format used to encode trees as text files
uses simple parantheses to record the relationships between taxa
in the newick format you can have multiple trees in a single file by separating the trees with a semicolon ";" character:
hen you will want to alter the tree to represent different aspects of your dat
Phylo submodule gives you many tools for dealing with trees that are much easier than doing it manually
h branch tip are the taxa - these ends are referred to as terminal nodes
Phylo's tree objects provide the method .get_terminals() to get a list of all taxa in your tree.
Each terminal can have multiple attributes, including the branch_length and the name. We can access and alter these properties like this
If we want to root the trees we can choose the outgroup sequence and the root will be placed along the branch leading the outgroup.
you can measure the total branch length separating (AKA Distance) between any two taxa using the .distance() method
recorded branch lengths
mply provide the names of two taxa that you're interested in measuring as strings
remove taxa from your tree.
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