Assignment 6:

Load testseq4.msf into seaview, save as mase file 

To do so:

1) open the file in MS Word save as a text only file

2) fetch the file to your UNIX account

3) Start the X-Windows server on your machine (check the x-windows hints if you need help with this)

4) telnet to your UNIX account

5) export the DISPLAY to your machine

6) type seaview

Only in case you have too much trouble click here and save and FTP the mase format directlyThis file contains several aligned 16S rRNA sequences.  You can consider the two archaeal sequences (HR and MC – if you want to research which sequence is what, go here) as an outgroup. 
This data set was assembled to illustrate long branch attraction:  the animal and fungal mitochondrial 16S rRNA (DROS HOME ASPE) are fast evolving, whereas the plant mitochondrial ones (Zea) are not.

load testseq4.mase into phylo_win
set options for distances (see hand-out)
set options for gaps
calculate trees by neighbor joining with and without pair wise gaps removed only - what is the default?
inspect tree explore the rooting and branch swapping options 
discuss tree topology
-- What is where?
-- Which are the mitochondrial sequences?
-- Why does the tree look like it looks?

Rerun the neighborjoining analysis with different distance corrections
run a parsimony analysis (+/-) transversion only option
and, if the machine runs sufficiently fast, do an ml analyses (do not do a bootstrap on these in class)

Did you find an algorithm that has the plant mitochondria with the animal mitochondria?  With which settings did you obtain this result? 

Do you get the same result, if you select only part of the alignment?  (Do this with only one algorithm and distance correction.)   

Get working on your student project.