{Salphycon} is a shiny app that extends the functionalities of the {phruta} R package. {Salphycon} is able to (1) find potentially (phylogenetically) relevant gene regions for a given set of taxa based on GenBank, (2) retrieve gene sequences and curate taxonomic information from the same database, (3) combine downloaded and local gene sequences, and (4) perform sequence alignment, phylogenetic inference, and basic tree dating tasks. Both {phruta} and {salphycon} are focused on species-level analyses.
I live version of salphycon is currently hosted here. Please note that the server is farly slow and that the author is still working on adjusting the release to the constrains imposed by the server.
The phruta R package is designed to simplify the basic phylogenetic pipeline. All the code is run within the same program and data from intermediate steps are saved in independent folders (optional). phruta retrieves gene sequences, combines newly downloaded to local gene sequences, performs sequence alignments, and basic phylogenetic inference.
The main functions in the phruta R package and salphycon allow for a quick mining and curation of GenBank sequences. This package is designed for students and researchers interested in generating species-level genetic datasets for particular sets of taxa. Specifically, if you have a clade or group of species in mind, phruta will help you to assemble a molecular dataset with information available in GenBank. Note that phruta is more flexible than the functions implemented in salphycon.
phruta and salphycon simplify the phylogenetic pipeline, increases reproducibility, and helps organizing information used to infer molecular phylogenies.
Salpicon is sort of a fruit salad in Colombian Spanish. Salphycon intends to expand the functionality of phruta, from the Fruta is the Spanish word for Fruit and ph for phylogenetics, for multiple simulatenous searches across different taxonomic groups.
Please see our contributing guide.