Useful tools
Nucleic Acid Research Bioinformatics Links Directory
Genome browsers
  • The UCSC genome browser is probably the most popular, and includes the Galaxy service.
  • The ECR browser is ran by the NCBI.
  • NCBI's CCDC allows for interactinvely looking at the AA coded by each codon. You have to go to their website, type the gene name, and in the results press the "C" red link under "links".
Genomic repositories
  • NCBI powerscripting is a useful engine that allows to massively work on the NCBI database. A tutorial can be found here. A tool for building the URL commands and testing the pipelines can be found here.
Sequence Analysis
  • A server that plots sequence logos is Weblogo.
Service software
  • We use MSSQL as our database server. A tutorial can be found here. Matlab can connect to this server with the help of its DB toolbox.
  • We use Tortoise for code sharing in developing Matlab toolboxes and perl modules. A tutorial on how to use it can be found here.
Lab books
Evolution and Molecular Evolution
  • Lindell Bromham. Reading the story in DNA. Oxford University Press (2008).
  • Sean B. Carroll. The making of the fittest. W. W. Norton and Company (2006).
  • Jerry A. Coyne. Why evolution is true. Penguin books (2009).
  • Scott Freeman, Jon C. Herron. Evolutionary analysis. Pearson Prentice Hall, 4th edition (2007).
  • Phillippe Lemey, Marco Salemi & Anne-Mieke Vandamme (eds). The phylogenetic handbook. Cambridge University Press, 2nd edition (2009).
Pattern Recognition
  • Christopher M. Bishop. Pattern recognition and machine learning. Springer (2006).
  • Richard Duda, Peter E. Hart & David G. Stork. Pattern classification. John Wiley & Sons, 2nd edition (2001).
  • Sergios Theodoridis & Konstantinos Koutroumbas. Pattern recognition. Elsevier, 4th edition (2009).
  • Randal L. Schwartz, Tom Phoenix & Brian D. Foy. Learning Perl. O'reilly, 5th edition (2008).
  • Randal L. Schwartz, Brian D. Foy & Tom Phoenix. Intermediate Perl. O'reilly, 2nd edition (2006).
  • Larry Wasserman. All of statistics. A concise course in statistical inference. Springer (2010).
  • Jerrold H. Zar. Biostatistical analysis. Prentice Hall, 5th edition (2010).
Specific projects
Deep Sequencing with SOLiD
  • A good introduction to the SOLiD sequencer can be found here. A good summary of analyses tool is found on the ABI's website, here.
Lab administration
Lab meetings / Journal Clubs
Dan Reshef

Eitan: Project description
Interesting Seminar Clubs
Remote access to our server
This is what you should do to enter the lab's server from home:
  1. Run mstsc.
  2. Enter Server IP:
  3. Login using your regular username/password of the lab.
Remote access to the Linux Workstation
Remote access is the favored method of connection, as it does not block other users from using the computer.
  1. Have a login on the workstation. Contact Danny (20046) if you don't have one.
  2. Establish connection using putty on your PC desktop.
  3. The workstation IP under the "Host Name" in Session, is -> (SSH only, telnet NOT available).
  4. User name -> aka you user name on the workstation. not on the PC, they are different things!
  5. Use the workstation to your needs.
LifeScope license
user: carmelab
password: C@rm31!
Grocery store at campus
Our client number is 538.