1st. Edition EG1-LEG/UM5 @ Faculté des Sciences Rabat, June 10-14, 2019.
Hi, I'm Pablo Vinuesa and work as a professor @ Center for Genome Sciences from the Universidad Nacional Autónoma de México - UNAM.
Mi research lines integrate genomics and bioinformatics with molecular genetics and biology to study the evolution and raise of opportunistic nosocomial pathogens from environmental bacteria.
They are distributed from this GitHub repository and include the slides, exercises and data that will be used in the course. These materials were compiled from those I've developed over the years to teach diverse courses at the Universidad Nacional Autónoma de México - UNAM. The current version of the materials is written in Spanish. Future versions will be progressively translated to English.
I'm releaseing these materials EG-LEG-UM5 to the public domain through this GitHub repository under a No Comercial Creative Commons 4.0 License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0
If you have git installed on your machine, you can clone the repo by issuing the following command:
git clone https://github.com/vinuesa/Evolutionary_Genomics1-LEG-UM5.git
On ubuntu (and other Linux) machines it is very easy to install git:
sudo apt install git
Each chapter has an introductory section describing the key concepts underlying the diverse bioinformatics and evolutionary gentics topics under discussion, followed by one or more hands-on practical sessions. The course will walk you through the basics of homology searching on local machines (formatting of sequence databases for BLAST searches), multiple sequence alignment and phylogenetic inference under the maximum-likelihood and Bayesian optimality criteria, progressing towards microbial pan-genome analysis and phylogenomics.
Classes will take place from 9:00 to 13:00 and 14:30 to 18:00, Monday 10th to Friday 14th, at the Faculté des Sciences - UM5, Rabat, salle des actes, with the following schedule:
- Basic concepts in evolutionary biology and phylogenetics (theory)
- Introduction to Linux (computer lab)
- BLAST searching from the command line (computer lab)
- Multiple sequence alignment (computer lab)
- Introduction to phylogenetics, gene trees and species trees (theory)
- Research seminar by Pablo Vinuesa: The evolution of resistance and virulence in multidrug-resistant opportunistic pathogens: a phylogenomic approach.
- Substitution models and phylogenetic inference under the maximum likelihood criterion (theory)
- Model fitting and phylogenetic inference under the maximum likelihood criterion (computer lab)
- Bayesian phylogenetics (theory and computer lab)
- Discussion with students and Faculty, on research projects
- Computing homologous gene families from genomic data (theory)
- Pan-genome analyses with GET_HOMOLOGUES (computer lab)
- Inferring genome phylogenies from core- and pan-genomes (theory)
- Estimating genome phylogenies with GET_PHYLOMARKERS (computer lab)
To follow the course practicals, you will need to install the following software on your laptop/computer, preferably under Linux:
- clustal omega
- paup*
- phyml - binaries
- phyml - src code at GitHub
- Seaview (alignment editor and multiple phylogenetic methods)
- jModelTest2
- FigTree (visualize and edit trees)
- MrBayes
- GET_HOMOLOGUES
- GET_PHYLOMARKERS
suggestions for running a shell on Windows and a decent text editor, if you don't have access to a Linux machine
Work in genomics is mostly performed on UNIX or GNU/Linux servers. It is therefore essential to work proficiently in these environments. Therfore:
- all practical sessions will be run using GNU/Linux as the operating system
- we'll start the course by learning basic Linux commands and Bash programming
2.3 Computer lab 2. Fetching FASTA sequences from GenBank with ENTREZ parsing of files using the Linux filtering toolbox
- slides - pdf
- computer lab1 - commands
- computer lab1 - 16S_4blastN.tgz
- computer lab1 - gene_discovery_and_annotation_using_blastx.tgz
Block 5: Introduction to phylogenetic methods and modeling of sequence evolution: theory and practice
- slides: overview of phylogenetic methods - pdf
- slides: phylogenetics under the ML criterion - pdf
- computer lab phyml - tgz
- computer lab jModelTest2 - tgz
This block could not be taught in the 1st version of the course, because the associated software requires a full Linux installation. For those interested in working on this block by themselves, I'm providing links to the online tutorial for GET_HOMOLOGUES and GET_PHYLOMARKERS.
