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
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?
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.
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
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.
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.