Assembling and editing Sanger sequence

In this tutorial you will take typical raw sequence data produced from a Sanger sequencing run and learn how to edit and align chromatograms for downstream analyses such as building a phylogenetic tree or calculating nucleotide diversity. The tutorial covers bulk trimming of poor-quality sequences, editing sequences from alignments or assemblies, finding heterozygote and incorrectly called bases, and building consensus sequences from forward and reverse reads of the same gene.

In Exercise 1, you will edit and align a set of mitochondrial DNA sequences from the blue tit Cyanistes teneriffae.

In Exercise 2, you will edit and assemble the forward and reverse reads of a nuclear gene sequence from three reed warbler species.

This tutorial requires the Heterozygotes plugin to be installed. To install this, go to Tools→Plugins, find it in the list of available Plugins and click Install.

If you want to open the tutorial in a different window, click the new window button . If you prefer to view this tutorial on the web, click here.

Thanks to Martin Stevander and Maren Wellenreuther of Lund University, Sweden, for providing the source material and original design for this tutorial. The sequence data provided with this tutorial is for educational purposes only.