ClipKITSince the early 1990's, there has been one predominant guiding light for multiple sequence alignment trimming - the removal of phylogenetically uncertain or highly divergent sites; however, the efficacy of this approach has been called into question. ClipKIT implements an alternative strategy wherein sites with phylogenetic certainty are retained and others are removed. Our benchmarking analyses show that ClipKIT is a reliable and top performing software.
treehouseSometimes phylogenies are so large it is challenging to determine the relationships among a subset of taxa. To remedy this issue, treehouse, a user friendly shiny app, allows users to obtain subtrees from larger phylogenies. To obtain subtrees, the user must upload a list of tip names they want from a user inputted phylogeny or a phylogeny from the treehouse database. Thereafter, the user can download a pdf or newick file of the phylogeny with only the tips of interest.
JPEG2ColorPalJPEG2ColorPal takes as input a JPEG and an integer, (n). As output, the software plots a color palette with n colors as well as the hex codes of every color generated.