Question: Using BioPerl to create Phylogenetic Tree
gravatar for Andrea
5.3 years ago by
Andrea40 wrote:

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 im not really sure how to select these proteins and what the format of the input file should be. Also wich bioperl modules should i use?Any suggested worflow about my task or any source of help that i can use?

Im really new in the Wolrd of bioinformatics.I would appreciate any advice given!

Thanks in Advance!



ADD COMMENTlink modified 5.3 years ago by SES8.3k • written 5.3 years ago by Andrea40
gravatar for SES
5.3 years ago by
Vancouver, BC
SES8.3k wrote:

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.

ADD COMMENTlink written 5.3 years ago by SES8.3k

can you pleaze tell me which modules sould i follow.I have to complete this task using bioperl alone.


ADD REPLYlink modified 5.2 years ago • written 5.3 years ago by Andrea40
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