Table of Contents
Welcome!
This page contains the practices sections for the course :
Molecular Evolutions, Phylogeny, Phylogenomics and Adaptation
By François Serra, Leonardo Arbiza1) & Hernán Dopazo
from the Bioinformatics Department of the Principe Felipe Research Center. Valencia, Spain.
Getting Started
- In this tutorial we will be working on computers running under GNU/Linux. If you are not familiar with the most basic commands of this operating system please run through the GNU/Linux tutorial section.
- Bellow you will find links that we will be using throughout the course which are provided for easy reference. Remember that you can return to this page by clicking on the link to the 'Welcome!' page in the Main Menu in the upper left portion of this guide.
- The main PDF with the Evolution and Phylogenetics part of the Lecture material for the course, and the Adaptation part.
- The Phylemon server which is a suite of web-tools for molecular evolution, phylogeny, and phylogenomics.
- Do not forget to visit the Joseph Felsenstein list of phylogeny programs...!!!
- In order to run many of the programs in this course we will use four sample files containing DNA and protein sequence alignments and their respective trees. Please go ahead and download these to your computer now in to a location on your hard drive where you may easily retrieve them to run the exercises (e.g.: '~/phylo/.').
| Alignment files | Tree files | description |
|---|---|---|
| dna_seqs.txt | dna_tree.txt | DNA Alignment in sequential phylip2), tree in newick format |
| dna_seqs.nexus | XXX | nexus format, with Mr Bayes commands |
| protein_seqs.txt | protein_tree.txt & protein.2trees.txt | alignment in interleaved phylip format, tree in newick format |
Additional Pointers
- The main menu will be available through all pages in this guide in the upper left portion of all pages
- Go ahead and click on any of the items in the Main Menu and explore the different sections
- Look for further links in brown to section subparts.
- The small area right under the comic icon in the header section which says 'Trace:»…' will show the different tabs you have navigated into and makes returning to previously visited sections easier.
- The 'Table of contents' on the upper right part contains quick links to the different sections of each page.
- The search bar at the bottom right, is quite useful. i.e. try searching for 'dnadist'
- Ooh, and please visit this Credits section to learn about the people involved and software used. Some additional tips are also provided there!
That's it ;)
Hope you enjoy!!
1)
original designer of this tutorial
2)
PHYLIP accepts two main formats, sequential and interleaved. Sequential means that all the characters (bases) of each taxon follows the name of that taxon in a single block. Sequential is the simplest format to deal with, as it allows you to quickly add or delete taxa- however unless you have only one line of characters it is not possible to see that the characters are reasonably aligned.
