William D. Lees and Adrian J. Shepherd, “Utilities for High-Throughput Analysis of B-Cell Clonal Lineages,” Journal of Immunology Research, vol. 2015, Article ID 323506, 9 pages, 2015. doi:10.1155/2015/323506
Please contact the author, William Lees, at firstname.lastname@example.org,bbk.ac.uk if you have questions or suggestions.
My AnnotateTree run did not produce a tree? Please check the 'Logs' tab on the results page to see what the problem was. Please check that each sequence is included exactly once, that no sequence ids are duplicated, and that the tree definition is not corrupted.
How long will my job take to run? Most jobs will finish within a few minutes, but jobs may take longer if multiple requests are received in a short space of time. Requests are queued and satisfied one at a time in order to prevent the server becoming overloaded
Can I use Germline with junction analyses from a source other than IMGT? Yes. Please save the results of the junction analysis in comma-separated or tab-separated format. You can download examples for the light chain and heavy chain.
Why don't you provide built-in support to infer the phylogenetic tree? A number of command line and web-based tools are available: for example the web-based version of IQ-TREE. We feel that it is best to commit our web-based resources to the specifics of annotation and germline derivation, and to emphasise the freedom to select a phyogenetic inference method that is suited to the particular task at hand.
I am told that my request is too large? The web versions of AnnotateTree and Germline are limited to 200 sequences at most, in order to prevent this free resource becoming overloaded. If you wish to run larger analyses, please consider downloading and installing the command-line tools.
X server errors. On Linux, AnnotateTree requires access to a web server in order to render phylogenetic trees. If an X server is not available, the analysis will still complete, but image files will not be created. If necessary, you can provide a standalone X server such as xdm, as suggested in the ETE documentation here. In this case, you will also need to configure the DISPLAY environment variable to point to the X server: set DISPLAY=localhost:0.0