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BioPython for create ancestrals seqvences

Semestral project to BIF on BUT FIT

Create ancestrals amino acides seqvences for Phylogenetic tree

Used packages

  • BioPython
  • Pandas

Run

just start main.py using python3 interpreth

python3 main.py

Need files

for run program prgram need some files. This files can be chaged in top of python script.

TREE_FILE       = "tree.tre"
MSA_FILE        = "msa.fasta"
ANCESTRALS_FILE = "ancestrals.csv"
OUT_DIR         = "output"
  • TREE_FILE contains fylogenetic tree in Newick (with confidence)
  • MSA_FILE cantains aligmented leaves seqvences in FASTA
  • ANCESTRALS_FILE contains posterior probabilty of every aminoacid in every seqvence