Question: Creating A Phylogenetic Tree From A Multiple Sequence Alignment.
gravatar for Caitlin
4.9 years ago by
Caitlin90 wrote:

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.


multiple-alignment • 13k views
ADD COMMENTlink modified 4.8 years ago by sebabiokr10 • written 4.9 years ago by Caitlin90

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?

ADD REPLYlink written 4.9 years ago by cts1.6k


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

ADD REPLYlink written 4.9 years ago by Caitlin90

Muscle produces fasta format by default. Try paste your alignment there (It's gene's and not proteins, right ?):

ADD REPLYlink written 4.9 years ago by Olivier440
gravatar for cts
4.9 years ago by
cts1.6k wrote:

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:

ADD COMMENTlink written 4.9 years ago by cts1.6k

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 many phylogenetic analysis tutorials on the web may also be helpful:

ADD REPLYlink written 4.8 years ago by Hamish3.0k
gravatar for musta1234
4.9 years ago by
musta123410 wrote:

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

ADD COMMENTlink written 4.9 years ago by musta123410
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