The protocol used for constructing alignments and trees for the gene families in LIS has been developed into a service to enable users to submit their own sequences to be added to the trees for these families.
Through the previously released functional annotation tool, gene family assignments are made using HMMER to find the best gene family match out of the subset of phytozome 10.2 Angiosperm gene family models for which LIS-managed genomes have one or more members. These gene family assignments are listed in the table of annotations for the sequences. To initiate the computation of multiple sequence alignments (MSA) and phylogenetic trees for a family, click on the "tools" icon next to the gene family link in the table. This will include all the user submitted sequences assigned to the given family in a single execution of the services, resulting in a view of the gene family phylogeny that is based on the standard LIS phylotree view (including access to the underlying MSA). More details on the services underlying this feature can be found in the lorax code repository.
Note that we have imposed an initial maximum time limit of 15 minutes for the tree calculation- this may be insufficient to enable construction of trees for very large families. Future releases of the tool will work to relax this restriction.
Other enhancements to the annotation tool include making InterPro analyses optional for faster lightweight annotation, the inclusion of more information in the summary table and the use of DataTables to enable sorting and filtering of the summary information.