Rhone-Alpes Bioinformatics Center


A Simple Phylogenetic Tree Construction pt. 2

Example 1 : Identifying an unknown bacterial sequence

Problem :

-  Phylogenetic techniques are often used in many diverse fields of science, such as medicine, archaeology, criminology, microbiology, etc. When presented with an unknown sequence, phylogenetics is the best tool available to identify this sequence and place it in comparison to others.
-  In this example we are presented with an unknown proteobacteria from an Environmental sample. By building a phylogenetic tree with other proteobacteria sequences, we will try to identify the unknown sequence’s Class (alpha, beta, delta, epsilon, or gamma).

Objectives :

-  Understand the method used in identifying an unknown sequence.
-  Understand the limitations of this method
-  Get to grips with various software (CLUSTALw, SeaView, Phylo_win and Njplot)

STEP 1 :

texte - 32.1 ko
FASTA Sequences

STEP 2 :

STEP 3 :

STEP 4 :

- The tree seems to show that our environmental sample sequence is in fact a betaproteobacteria because its is clustered with all other betaproteobacteria with 100% bootstrap support. Further identification of the environmental sequence would require more sampling within betaproteobacteria.

STEP 5 :