Software

PURC: Pipeline for Untangling Reticulate Complexes

I am the main developer of PURC, a pipeline for inferring the underlying biological sequences (alleles, paralogs, or homeologs) from amplicon sequencing data (PacBio, Illumina, etc). It is geared toward analyzing polyploid species complexes but is also effective for other applications; the final output of a full run includes an alignment for each locus with each homeolog or allele sequence in the amplicon data labeled with the source sample information and amount of coverage.

Publication: Rothfels, C.J., K.M. Pryer, F.-W. Li. 2017. Next-generation polyploid phylogenetics: Rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. New Phytologist 213: 413-429. Reprint PDF

Source code available here.

Boechera Microsatellite Database 

Boechera (Brassicaceae) has many features to recommend it as a model genus for ecological and evolutionary research, including species richness, ecological diversity, experimental tractability, and close phylogenetic proximity to Arabidopsis. However, efforts to realize the full potential of this model system have been thwarted by the frequent inability of researchers to identify their samples and place them in a broader evolutionary context. We have developed the Boechera Microsatellite Website (BMW), a portal includes analytical tools that utilize data from 15 microsatellite loci as a highly effective DNA barcoding system. The BMW facilitates the accurate identification of Boechera samples and the investigation of reticulate evolution among the 83 sexual diploid taxa in the genus, thereby greatly enhancing Boechera‘s potential as a model system.

Publication: Li, F.-W., C.A. Rushworth, J.B. Beck, M.D. Windham. Boechera (Brassicaceae) Microsatellite Database: an online portal for species identification and hybrid relationship resolution. Database (in press). Reprint PDF

Source code available here