17
sep
Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg

An introduction to supersmartR

Develop pipelines in R for creating phylogenetic trees including mass sequence download, sequence identification, alignment, tree estimation, supermatrix and supertree construction.

We present a one-day workshop on a new platform for constructing
phylogenetic trees, supersmartR. Like its predecessor, SUPERSMART, this new program
aims to automate the process of phylogeny generation using a multiple-supermatrix and
supertree approach but works entirely within the popular R environment. For the latest
development information on supersmartR, check out its GitHub repository at:
https://github.com/AntonelliLab/supersmartR. In this workshop, we will present the
program as a whole and provide detailed tutorials for each of supersmartR’s individual
modules (phylotaR, restez, outsider …). By the end of the workshop participants will
have advanced their knowledge of R and learned how to identify and download
orthologous sequence clusters from R; construct non-time-calibrated phylogenetic trees;
download large subsections of GenBank to their local computer; and integrate non-R
software into R pipelines. It is expected that participants have basic working knowledge
of R and have experience of the tools required for constructing phylogenetic trees.
There is a possibility of taking a course on an introduction to R ahead of this workshop.

Fakta
Tid: 2019-09-17 09:00 - 17:00
Ort: Gothenburg
Lokal: Global Biodiversity Center, Carl Skottsbergs gata 22B
Arrangör: ForBio, Swedish LifeWatch, Biodiversity Atlas Sweden, and the Nordic e-Infrastructure Collaboration
Sista anmälningsdag: 10 september 2019
Mer information:

Course teachers: Dominic J. Bennett and Matthias Obst
Recommended background: Basic knowledge and experience in R and phylogenetics.
Course level: PhD level (motivated Master's students welcome)
Fee: No fee
Food: Lunch will be provided for all course participants
Application: A short motivation (5 lines stating goals and expectations) and a 1 page CV should be submitted to matthias.obst@marine.gu.se latest by 20th August 2019.
Contact: Dominic J. Bennett (dominic.john.bennett@gmail.com), Matthias Obst
(matthias.obst@marine.gu.se)



Kontaktinformation
Sidansvarig: ulrika.sehlberg.samuelsson@slu.se