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Computational molecular evolution

8 – 19 May 2016 | Heraklion, Greece

Application deadline

October 30, 2015

Selected participants will be notified by

December 1st, 2015

Payment deadline

February 15, 2016

Apply now!

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Major co-sponsor: Heidelberg Institute for Theoretical Studies

Host Institute: Ιnstitute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research

About the practical course

The need for effective and informed analysis of biological sequence data is increasing with the explosive growth of biological sequence databases. A molecular evolutionary framework is central to many Bioinformatics approaches used in these analyses. Additionally, explicit use of molecular evolutionary and phylogenetic analyses provide important insights in their own right, e.g., analysis of adaptive evolution in viruses providing clues of their interaction with host immune systems.

To this end, we aim to provide graduate and postgraduate researchers with the theoretical knowledge and practical skills to carry out molecular evolutionary analyses on sequence data. The course will entail data retrieval and assembly, alignment techniques, phylogeny reconstruction, hypothesis testing, and population genetic approaches. The course will cover sessions on analysis of both protein and nucleotide sequences, including NGS data. However, we do not cover traditional NGS analyses (e.g., QC, read mapping, variant calling, assembly etc.) .

Also, the EMBO Practical Course will offer a unique opportunity for direct interaction with some of the world-leading scientists and authors of famous analysis tools (Tanja Stadler, Tracy Heath, Olivier Gascuel, Nick Goldman, Bruce Rannala, Alexandros Stamatakis, Benjamin Redelings, Ziheng Yang, etc.) in evolutionary Bioinformatics.

Note that the last three courses in Crete were heavily over-subscribed. The expected participant acceptance rate is below 20%. Experience from previous years has led to preference being given to candidates who:

  • are doctoral candidates in the early to middle stages of their thesis research
  • already have some familiarity (i.e. have already used some of the relevant tools) with phylogenetic methods
  • have already collected/assembled a molecular sequence dataset to analyze in their work
  • have experience working in a Unix/Linux command-line environment

We will also select a small fraction of participants that already work in Bioinformatics labs, to intensify collaboration between early career stage Biologists and Bioinformaticians. Applicants from labs with a strong focus on computational molecular evolution methodology need to carefully outline their motivation for attending the course in this context, since they have ready access to expert supervision and are likely to be very skilled already in the topics we teach, or are in the course of becoming very skilled therein.







Application deadline

October 30, 2015

Selected participants will be notified by

December 1st, 2015

Payment deadline

February 15, 2016







Local Students

EUR 75




Registration fees include:

  • Non-local students: breakfast, lunch, dinner and accommodation
  • Local students from Crete only: lunch only

Please note that ALL trainees are required to:

  • present a poster during the course
  • be already familiar with using the Linux operating system prior to attending the course or, if not familiar, invest a substantial amount of time prior to the course in getting familiar with Linux (we can provide some help, i.e. a Linux installation on a CD, for those of you with access only to a Windows machine)


We strongly discourage applications of more than one student from the same lab.

To apply, students must upload a 2-page CV, a motivation letter, and a reference letter by their advisor.


Registration fee waivers

A limited number of non-local participants will be granted registration fee waivers.

In addition, one local and one non-local participant will receive a Margarita Metallinou fee waiver award.

Margarita Metallinou was a very talented and promising young evolutionary biologist with a passion for reptiles and taxonomy. She completed her PhD on the evolution of desert Geckos at the University of Barcelona and the Institute of Evolutionary Biology in 2014. Thereafter, she immediately started a postdoc at Villanova University in the US. Margarita was a participant at the first CoME course in Crete that took place in 2010. She was a brilliant and enthusiastic student, who captivated instructors and fellow participants with her thoughtful questions, her eagerness to learn, and her great spirit. She greatly enjoyed this course and it had an important impact on her subsequent career, both from a personal as well as scientific perspective. During her short but intense career, she inspired many students around the world with her dedication and passion for science, her tenacity, her boundless energy, her ability to help everyone around her, and her determination to enjoy life and follow her dreams. Her tragic end touched the entire scientific community and, in particular, the organizers, instructors, and former participants of this course.


This award is in memory of Margarita, who passed away in July 2015 while doing fieldwork in Zambia. Via this award we hope to transmit Margarita’s passion for research to future generations of students and to preserve her memory.



Applicants do not require to apply for these awards separately, selection of awardees will be handled directly by the organizers. Awardees will be informed directly.






Via IBAN bank transfer.







venue map


Main building of HCMR
71500 Gournes (former american base)
Heraklion, Crete, Greece


Hotel Astir Beach
Gouves, Heraklion, 70014, Crete, Greece

It takes approximately 15 minutes to walk from the hotel to the Institute.

All food (breakfast, lunch, dinner) and accommodation costs are included in the registration fee for non-local students.

The island of Crete is the largest of the Greek islands and separates the Aegean from the Libyan sea. Crete forms a significant part of the cultural heritage of Greece and retains its own local cultural traits; such as its own music and dialect. Heraklion is the largest city and the capital of Crete. Crete was the centre of the Minoan civilization, approximately 2600–1454 BC, which is the oldest Greek and European civilization. The Knossos palace, one of the two most important Minoan sites on the island, is located in the outskirts of Heraklion. The archaeological museum in Heraklion contains some of the most important treasures of minoan culture such as the Phaistos disk.
Apart from numerous magnificent beaches Crete is characterized by a very diverse landscape and three high mountain ranges (all rise to above 2000 meters from sea-level), that provide excellent hiking opportunities and views on spectacular gorges such as the Samaria Gorge.
Among the most famous sons of the islands are the writer Nikos Kazantzakis, the painter El Greco and the poet Odysseas Elytis (Nobel Prize in Literature). Famous musicians are Nikos Ksilouris and his brother Antonis Ksilouris (also known as Psarantonis).



The Ιnstitute of Marine Biology, Biotechnology and Aquaculture (IMBBC) of the Hellenic Centre for Marine Research (Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR) ) is located about 15km east of Heraklion airport which is the main airport of the island. The Institute is located right next to the Cretaquarium in a small sea-side town called Gouves.




  • Change planes at Athens airport, there are about 10 daily flights from Athens to Heraklion.
  • Since the tourist season will already have started in May there is a good chance of finding a direct non-stop charter flight to Heraklion from many central European countries.
    For example Easyjet offers direct nonstop flights from London. We suggest that you use google flights for finding non-stop flight to Heraklion


Getting from Heraklion Airport to Gouves:

Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR) map can be downloaded here.
How to get from Heraklion Airpot to IMBBC/Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR) - CRETAQUARIUM at Gournes.



There is a bus leaving approx every 30 minutes from Heraklion Airport to Gournes.
Look for departures from the port of Heraklion (stopping at the airport, arriving there 5-10 inutes after departure from the port) to Chersonissos, Maila, Ag. Nikolaos, Sitia:
Ask the bus driver for a stop near by the Cretaquarium or the Hotel.

Heraklion Main Bus Terminus = tel.: +30 2810 246530

Ticket price (2015) = 2.00 EUR (one way)
Travelling time = approx. 20 minutes



By following the special brown information signs "CRETAQUARIUM", posted on the national road and several minor roads linked to it.



Lastly, those who prefer to come by taxi but couldn't find any available at the Airport Heraklion, could call:

  • Heraklio radio taxitel.: 2810 210102 -168 -146
  • Candia radio taxi tel.: 2810 361362 -3 -4

Indicative 2015 taxi fare:

  • Heraklion Airport to Heraklion Center 10,00 €
  • Heraklion Airport to Gournes 25,00 €
  • Port of Heraklion to Heraklion Center 6,00 €
  • Port of Heraklion to Gournes 25,00 €

Extra 2015 taxi charges:

  • Port extra 2,10 €
  • Taxi call for appointment 3,40 €
  • Plain radio taxi call 1,20 €.
  • Plain radio taxi call 1,70 €.

Taxi trips after midnight will cost 2-3 EUR more per trip.

You can also book a taxi on-line via
(contact tel.: +30 6937 333 730)

When making your booking, you must mention the phrase "ELKETHE - Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR) " (Host Center) and your destination (e.g., Astir Beach Hotel). You will get a special discount fare and pay a fixed prize of 25 EUR from the airport to the Hotel at Gournes (including taxes and airport & luggage charges). There are no extra charges for after-midnight transfers or delayed flights.

After filling in the online form, you should receive a confirmation e-mail within 2-10 hours, with all required information.

All taxis are Mercedes with English-speaking drivers.