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Slides day 1
Exercise 1 - Parameter estimation
Exercise 2 - Tree topologies
Exercise 3 - Model comparison
Exercise 4 - Branch support
Exercise 5 - Command line
Exercise 6 - Inferring ML phylogenies with codon models
Exercise 7 - Inferring ML phylogenies using real datasets
Exercise 8 - Re-Analyze published datasets
Welcome
Schedule
| Time | Topic | Lecturer |
|---|---|---|
| 08:30 - 09:30 | Markov models of substitutions | Maria |
| 09:30 - 10:00 | Practical: Data formats and visualisation | Lorenzo |
| 10:00 - 10:30 | Break | |
| 10:30 - 11:30 | Hypothesis testing, model selection | Maria |
| 11:30 - 12:00 | Practical: Hypothesis testing, model selection with PHYML | Lorenzo |
| 12:00 - 13:30 | Lunch | |
| 13:30 - 14:15 | Practical: Tree-thinking quiz (in small groups) | Maria (?) |
| 14:15 - 15:15 | Phylogenetic inference | Maria |
| 15:15 - 15:45 | Break | |
| 15:45 - 17:00 | ML tree inference: Exercises with PHYML | Lorenzo |
| 17:00 | The end |
| Time | Topic | Lecturer |
|---|---|---|
| 08:30 - 09:15 | Natural selection and codon models | Maria |
| 09:15 - 10:00 | Practical: Exercises with PAML (basics, one ratio model) | Lorenzo |
| 10:00 - 10:30 | Break | |
| 10:30 - 11:15 | tba | Maria |
| 11:15 - 12:00 | Practical: Exercises with PAML (branch models) | Lorenzo |
| 12:00 - 13:30 | Lunch | |
| 13:30 - 15:00 | Site models, detecting residues under selection | Maria |
| 15:00 - 15:30 | break | |
| 15:30 - 17:00 | Practical: Exercises with PAML (site models) | Lorenzo |
| 17:00 | The end | |
| 17:15 | After the course, we will head to a pub in town for anyone who fancies joining! |
| Time | Topic | Lecturer |
|---|---|---|
| 08:30 - 09:15 | Introduction on episodic positive selection | Maria |
| 09:15 - 09:45 | Practical: Detecting episodic positive selection using small dataset | Lorenzo |
| 09:45 - 10:05 | Break | |
| 10:05 - 10:30 | Small introduction on how to design a computational pipeline for phylogenetic analyses | Maria |
| 10:30 - 11:00 | Practical: Tutorial session on how to build pipelines | Lorenzo |
| 11:00 - 12:00 | Open Q/A session + hands-on using participants’ datasets |
Installation
Software
Phylogenetic tree reconstruction
Positive selection analyses
Sequence alignment visualizers
Tree visualizers
Tutorials
Download ZIP File Download TAR Ball Clone from GitHub
Licence
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. Except as contained in this notice, the name(s) of the above copyright holders and institutions shall not be used to endorse or promote products derived from this software without specific prior written permission.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
This project is maintained by gattil