Since 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.
Sometimes 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.
Creating publication ready figures can increases figure accessibility and improve science communication. Here, I present ggpubfigs, an R package with customized themes and color blind friendly color palettes to help create publication (or presentation) ready figures. Please contact me if you would like to contribute a theme or color palette!
JPEG2ColorPal 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.