/upgma_phylogenetic_tree

Scripts in Python to read nucleotide/protein sequences and construct Phylogenetic relationship using UPGMA

Primary LanguagePython

UPGMA-Phylogenetic-Tree

To run,

Question 1

python Q1a.py
python Q1b.py

Question 2

python Q2a.py
python Q2b.py

The UPGMA algorithm used is the one from Wikipedia
https://en.wikipedia.org/wiki/UPGMA

Question 1

Construct a phylogenetic relationship for the given nucleotide sequences(Nucleotide.txt)

  • 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'
    For example:
    seq1 = 'ATGCATGCAA'
    seq2 = 'ATGCATGCTA'
    Distance(seq1,seq2) = Mismatches/total length = 1/10 = 0.1
  • Write a script that uses 'Ndistance.txt' and generate phylogenetic relationship between the organisms using UPGMA method.

Question 2

Construct a phylogenetic relationship for the given protein sequences(Protein.txt)

  • 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'. Use 'BLOSUM62.txt' for getting score values.
    For example:
    seq1 = 'AGYFKTP'
    seq2 = 'GRKLYSK'
    Score(AG) = 0, Score(GR) = -2 and so on
    Distance(seq1,seq2) = Score(AG) + Score(GR) +....
  • Write a script that uses 'Pdistance.txt' and generate phylogenetic relationship between the organisms using UPGMA method.