Lab 4 - Trees-Copy1 - Jupyter Notebook

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• 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.