Creating A Phylogenetic Tree From A Multiple Sequence Alignment.

Question

[Caitlin]

Hi all.

I have used muscle (3.8) to perform a multiple sequence alignment on 635 tumor suppressor gene sequences and edited (via perl) the output file so it conforms with FASTA. I would like to generate a phylogenetic tree from the msa file. I am enrolled in an introductory level bioinformatics / scientific computing course at a local community college and this would directly relate to my semester project requirement.

Thanks for the help.

Caitlin

[cts]

Your question does tell us what it is that your having problems with? Do you just want to know which tree building software to use?

[Caitlin]

Hi.

Yes, please. Being a fledgling bioinformaticist, I am quite eager to learn what tool(s) would be most appropriate for the task described above.

[Olivier]

Muscle produces fasta format by default. Try paste your alignment there (It's gene's and not proteins, right ?): http://mobyle.pasteur.fr/cgi-bin/portal.py#forms::dna_phylogeny_methods_comparison

[shiheng0828]

Hi, how did you finish this part? I also have to Create A Phylogenetic Tree From A Multiple Sequence Alignment. It's urgent project. Hope you can read it soon. Thank you.

[Ram]

Hi,

Please do not add answers to existing questions unless you're answering the question. The right thing to do would be to add a comment or open a new question and reference this one. You've opened a new question, so you might just want to edit it and add a reference to this post.

I'm moving your "answer" to a comment now.

Answer 1

[cts]

I think that the following link and references/links within is quite good for discussing the types of tree building approaches, and also mentions some of the software to use for each method as well: http://cshprotocols.cshlp.org/content/2008/4/pdb.ip49.full

[Hamish]

While the Cold Spring Harbour Protocols and Current Protocols in Bioinformatics are great for this, they do suffer from the disadvantage of requiring a subscription (hopefully your institution has one). However when these are not an option there are some other choices...

• The PHYLIP website is a useful source of information about phylogenetic tools (not just PHYLIP)
• Phylogeny.fr provides a quick and easy route to getting a phylogenetic tree
• Understanding Phylogenies from Evolution 101 provides a lay overview that introduces the core terminology

The many phylogenetic analysis tutorials on the web may also be helpful: http://www.google.com/search?q=phylogenetic+analysis+tutorial

Answer 2

[musta1234]

One good software especially for windows gui is MEGA 5.1, it allows you to run many of the basic tree-building algorithms: parsimony, neighbor-joining, maximum-likelihood etc. You can then compare your results and see. No guarantee it will work with 400 sequences though http://www.megasoftware.net/