Ortholog assembly with aTRAM for phylogenomic and species delimitation analyses

Course details

In this 11-hour course, participants will be introduced to the assembly of ortholog genes from low-coverage sequencing data using aTRAM.

The aim of the course is to train researchers in the most important aspects of the aTRAM pipeline in order to apply it to species delimitation and phylogenomic studies.

The course will combine theory with hands-on exercises using real datasets.

Language: English.

Number of places available: 18.

Instructor: Dr. Jorge Doña.

Target audience and requirements

Master students, early career researchers (pre-docs and post-docs), or senior researchers, either from Industry or Academia, interested in species delimitation and phylogenomics.

Basic skills in high-throughput sequencing are required. Researchers who are not familiar with high-throughput sequencing might want to consider signing up first to our introductory course. Basic use of UNIX-based command line is desirable.

Hands-on work will be performed in UNIX environments (Linux, Mac).

All participants should bring and use their own laptops.

Course program

10:00 - 11:30 Introduction to ortholog genes assembly using aTRAM Gene tree and species tree inference
11:30 - 12:00 Coffee! Coffee!
12:00 - 13:30 Reference panels, aTRAM libraries, locus assembly, and post-processing using aTRAM2 Practical session: gene tree and species tree inference
13:30 - 15:00 Lunch Lunch
15:00 - 16:30 Practical session: aTRAM2 Species delimitation analyses: barcode-gap-based and coalescence-based methods
16:30 - 17:00 Coffee! Coffee!
17:00 - 18:00 Phylogenomic analyses Practical session: species delimitation analyses
18:00 - 20:00 Free time Good bye!
20:00 - 22:00 Dinner and party



First edition 2019: October 24 - October 25.


The course will be held at Camping Los Manzanos. Los Manzanos is a singular and quaint place in the municipality of Oleiros (A Coruña, Galicia, Spain). It is located within walking distance of the picturesque XVI-century castle and the lively cafés in the village of Santa Cruz. Travellers who want to enjoy being near the sea, but not right on the sea itself, flock to this original campsite in the woods which is well-known for its restaurant and its sculptures and paintings by Julio Sanjurjo. A Coruña, one of the most beautiful cities in Northern Spain is only 12 km. away.

The easiest way to reach the venue from A Coruña airport is by taxi; alternatively, you may take the airport bus to A Coruña Bus Station and then take the bus line to Santa Cruz. Please do not hesitate to let us know if you need further information on how to get to Los Manzanos.


Course fee (including course materials and refreshments): 350 euros.

Course fee + accommodation and meals: 460 euros. This package includes accommodation in shared bungalows (2 or 4 people) with en suite bathroom (check in on Wednesday evening; check out on Friday morning) and meals (breakfast, lunch, and dinner) at the venue restaurant. The bungalows are equipped with bed linen and towels, TV, coffee maker, toaster, microwave oven, fridge, flatware, dishware, and heating. Additional accommodation options are available at an extra cost.

How to apply

If interested, please fill out our contact form and specify:

  • The course and edition you are interested in enrolling in.
  • The details of the paying institution (including VAT number).

The sign-up deadline is 30 days prior to the start of the course.

Please note that there is an 18 participant limit and applications will be accepted on a first-come, first-served basis.

A 10 participant minimum per course edition is required. If that minimum is not reached the edition will be cancelled and participants offered a different edition or a total refund.