A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using the multispecies coalescent and concatenation approaches

Fungal Identification Pipeline

This repository contains data and code from the manuscript, "Analysis of biodiversity data suggests that species are hidden in predictable places".

Official GitHub repository for the R package "Species Identity and Evolution in R" (spider)

An R Shiny App that assesses sampling effects (e.g. sample size and BEAST parameters) on GMYC output for species delimitation.

Scripts written in R

Molecular Sequence Manipulation Tools

This repository includes scripts and data used in Sgarlata et al., 2023 entitled "The Genomic Diversity of the Eliurus genus in northern Madagascar with a Putative New Species".

Clustering using Gaussian mixture modeling for species delimitation and classification

created to work on with data for the article

Biogeography and species delimitation of the rheophilic suckermouth-catfish genus _Pseudolithoxus_ (Siluriformes: Loricariidae), with the description of a new species from the Brazilian Amazon

R package to run GMYC analysis with subsamples of sequences obtained from within the species delimited using all sequences.