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Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and processes, and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 (and counting) functions that process MSAs and trees.
bioRxiv preprint; Documentation; Source code
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.
Publication PDF; Documentation; Source code
Orthofisher conducts automated HMMsearches among a set of proteomes using a predetermined set of orthologs. Sequence similarity searches classify results as multi-copy, single-copy, or absent in a given genome. For the purposes of phylogenomics/phylogenetics, multi-fasta files are generated for all sequences as well as those that are single-copy; for gene family copy number determination, easily parsed output files contain absolute copy number of hits from the sequence similarity search.
Documentation; Source code
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.
Publication PDF; Source code
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!