Tag Archives: Methods

Adding new sequences (Mistakes were made)

Looking through the tree produced in my last post, I noticed that several interesting sequences were missing from the tree. There are also less sequences in the tree than I get if I search for “Nostoc rbcX” in Entrez. Turns … Continue reading

Posted in Cyanobacterial photobionts | Tagged | 2 Comments

Adding host information to the Nostoc phylogeny

Having obtained 496┬áNostoc rbcX sequences (plus one outgroup) and used them to infer a reasonable phylogeny, all that is left is to assign host association information to the branches. This will require (a) parsing the sequence files to obtain host … Continue reading

Posted in Cyanobacterial photobionts | Tagged | Leave a comment

Obtaining the sequences

Perhaps not surprisingly given my background, I will be starting with Nostoc photobionts. In my opinion, the most useful marker for this group is rbcX, so I will be starting there. I have decided to use blast to obtain all … Continue reading

Posted in Cyanobacterial photobionts | Tagged | 1 Comment