Using BioPerl to create Phylogenetic Tree

Question

[Andrea]

Hi everyone,

My task is to create a Phylogenetic Tree using BioPerl. An input file that contains 10 protein IDs (or genes IDs) should generate an output file ,in newick form, with the final Phylogenetic Tree.

First of all I'm not really sure how to select these proteins and what the format of the input file should be. Also which bioperl modules should I use?Any suggested worflow about my task or any source of help that I can use?

I'm really new in the World of bioinformatics.I would appreciate any advice given!

Thanks in Advance!

Answer 1

[SES]

You cannot infer a tree directly with BioPerl, but you can run alignment and tree inference programs through the bioperl-run package. Since you are starting out, I recommend not going that route because that adds another layer of technical difficulty if you are not familiar with Perl/BioPerl. The basic steps are:

1. Create a FASTA file of your proteins.
2. Align these sequence using a multiple sequence alignment program like MUSCLE.
3. Generate a tree using one of four main paradigms for tree inference (Parsimony, ML, NJ, or Bayesian methods).
4. Convert the tree to Newick (if necessary) for plotting with BioPerl.

All of these steps can be done online, especially for 10 sequences. When you get to step four have a look at the BioPerl HOWTO page for saving images of trees. Also, consider using the separate Bio::Phylo package for phylogenomics work with Perl.

[Andrea]

Can you please tell me which modules I should follow. I have to complete this task using bioperl alone.