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Adding or editing 3D features (104 Kb)
Graphically adding and editing 3D features within Sockeye allows us to visualize diverse annotation. This document shows you how to create, add, and edit the 3D features in Sockeye.
Aligning C.elegans and C.briggsae within Sockeye (804 Kb)
This document describes how a user can create and visualize cross-nematode alignments within the 1.1 release of Sockeye.
Using Sockeye to perform multiple alignments (419 Kb)
Currently, we offer LAGAN for pairwise alignments, and Multi-LAGAN and CLUSTALW for multiple alignments. LAGAN and CLUSTALW can be run with default settings. To run Multi-LAGAN you will have to enter a schematic phylogenetic tree. Details of the tree format are given in the README.mlagan that is part of the LAGAN Toolkit source distribution. The distribution is available from its authors.
Adding new EnsEMBL connections ( 245 Kb)
Sockeye allows a user to connect to multiple EnsEMBL servers. This document shows you how to get your Sockeye installation to serve data from your own favorite EnsEMBL server.