PhylTree

Using the Unweighted Pair Group Method with Arethmatic mean(UPGMA) to make Phylogenetic Trees.

Input Data

• DNA sub-sequences have been given in the "Nucleotide_alignment.txt" file, for the first question.
  
• Protien sub-sequences hae been given in "Protein_alignment.txt" file for the second question.
• "BLOSUM62.txt" is to be used for the scoring function in the 2nd question.

Aim

1. Construct a phylogenetic relationship for the given nucleotide sequences.
a. Write a script to generate a distance matrix csv file for the sequences present in the data file. Name the distance matrix file as 'Ndistance.txt'.
b. Write a script that uses 'Ndistance.txt' and generate phylogeney relationship between the organisms using UPGMA method.

2. Construct a phylogenetic relationship for the given protein sequences.
a. Write a script to generate a distance matrix csv file for the sequences present in the data file. Name the distance matrix file as 'Pdistance.txt'.
b. Write a script that uses 'Pdistance.txt' and generate phylogeney relationship between the organisms using UPGMA method.

Procedure

• Scoring functions are used to generate a distance matrix in the part a. of the question.
• The distance matrix is used to get the Phylogenetic Trees using the UPGMA method in part b.