Hello,
I am trying to study the taxonomic distribution of orthologous proteins of a given protein sequence ("query") in bacteria.
I have run a BlastP research using the aforementioned query to screen the non-redundant protein database, restricted to bacteria or subclades of particular interest and so I got a list of subjects ranked by homology.
Is there an automated method (either online tool or standalone software) to classify these sequences by taxonomy, thus getting a phylogenetic tree?
It would be great (if possible), then, to interactively navigate the taxonomic tree, expanding or contracting the identified subclades.
I tried the "Distance tree of results" functionality of Blast but it seems to me that it classifies sequences by their relative evolutionary distance (sequence similarity), which is not what I'm interested to obtain.
Thank you in advance.
You have two problems, first you don't have a taxonomy for the sequences and second is you are making trees. FIrst classify the sequences with the help of a reference database. Second step would be proceeding towards the phylogenetic tree.
The first step in constructing a phylogenetic tree is to select homologous sequences as computational data. This step actually involves two processes: one is to collect sequence data, and the other is to determine the homology of the data. The most commonly used alignment tools are Blast, Clustal, Muscle and FASTA.
There are many software packages available for phylogenetic tree inference and reliability testing, as well as Unifrac and ITOL tools for drawing and analyzing trees online. The most commonly used software are PHYLIP, MEGA and MrBayes.
Hope it helps!
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Programming Languages
- Python