BioComputing

P9 Online Data Bases

Synopsis: Using data from P8, construct phylogenetic trees for each alignment; evaluate phylogenetic trees, alignments, and chosen gene; submit your results in the form of a written paper.

General Procedures:

• Launch MacClade
• import fasta alignment (File->Open File)
• open tree window (Windows->Tree Window)
• construct hypothetical tree (Move Branch Tool)
  • store tree (Trees->Store Tree)
• construct clustal average distance tree (Move Branch Tool)
  • root tree (Reroot Tree Tool)
  • store tree (Trees->Store Tree)
• construct shortest (MacClade) tree (Search Above Tool)
  • store tree (Trees->Store Tree)
• compare trees
  • chart (Chart->Compare 2 Trees)
  • tree length, CI, RI (∑->Tree Length, Consistency Index, Retention Index)
• compare alignments
  • taxa (Taxa->Taxon List)
• compare changes
  • trace (Trace->Trace All Changes)
• Save your MacClade Nexus file to your flashdrive with a .nex extension!
• Repeat the entire procedure with your MAFFT alignment.

Assignment:

Submit your project in the form of a written paper; all papers require a title page, 1 inch margins, 12 pt font, and double-spacing.

All papers should consist of 3 parts:

• First, state the objectives of your project (i.e., What are you attempting to accomplish?)
• Second, summarize the methods you used to accomplish your objectives. Provide sufficient detail to allow your procedures to be repeated by someone else.
• Third, provide your results and a BRIEF evaluation of the project.

In your evaluation, please address the following:

• Which method of alignment is better? Why?
• Which method of tree construction is better? Why?
• Was the gene you chose appropriate for your analysis? Why?
  • Did it effectively resolve closely related taxa?
  • Did it effectively resolve distantly related groups?
• What can you conclude about the evolution of your gene from this assignment?

Supporting Links

Demo Files

.... Demo Files Download

Web Sites

.... MacClade MacClade Homepage