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andand authored Sep 30, 2023
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# Programming Lab P4 - Making a tree using UPGMA clustering

Hierarchical clustering is widely used in bioinformatics. In the CB2442 course, you have encountered it both in the Sequence feature module and in the Phylogenetics module. In this lab, your task is to write a function that, given a pairwise distance matrix and a list of names of the corresponding objects (in this case, sequences), performs hierarchical clustering using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method. The function should output the result as a tree in the [Newick](https://en.wikipedia.org/wiki/Newick_format#:~:text=In%20mathematics%2C%20Newick%20tree%20format,Maddison%2C%20Christopher%20Meacham%2C%20F.) format.
Hierarchical clustering is widely used in bioinformatics. In the CB2442 course, you have encountered it both in the Sequence feature module and in the Phylogenetics module. In this lab, your task is to write a function that, given a pairwise distance matrix and a list of names of the corresponding objects (in this case, sequences), performs hierarchical clustering using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) method. The function should output the result as a tree in the Newick format.

### Installation

Expand All @@ -20,7 +20,7 @@ In the `labp4.py` file, modify the function
```python
def upgma(dist_matr, names_list):
```
that takes a pairwise distance matrix (a 2-dimensional [numpy array](https://www.w3schools.com/python/numpy/numpy_creating_arrays.asp)) and a list of sequence names (a [list](https://www.w3schools.com/python/python_lists.asp)) as input and returns a tree in newick format. Also, set the list `authors` to contain all the group members names.
that takes a pairwise distance matrix (a 2-dimensional [numpy array](https://www.w3schools.com/python/numpy/numpy_creating_arrays.asp)) and a list of sequence names (a [list](https://www.w3schools.com/python/python_lists.asp)) as input and returns a tree in [Newick](https://en.wikipedia.org/wiki/Newick_format#:~:text=In%20mathematics%2C%20Newick%20tree%20format,Maddison%2C%20Christopher%20Meacham%2C%20F.) format. Also, set the list `authors` to contain all the group members names.

### Test

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