Bioinformatic Tools and Resources
We provide several free bioinformatic pipelines, scripts, and other software useful for a broad range of biology, ecology, genomics, and population genetics projects.
Check out our Blog for bioinformatics tutorials and how bioinformatics and systematics approaches are used to gain insight into native ecosystems, conservation, natural products and agricultural markets.
SORTER2-Tookit (Sort Orthologous Regions for Target Enrichment Reads, v2.0 Toolkit) is a modular set of python scripts designed to process and assemble target-capture datasets having hybrid and non-hybrid organisms. SORTER2-Toolkit helps users generate orthologous alignments when paralogs are present, phasing of sequences into respective haplotypes, and phasing of putative allopolyploid or homoploid hybrids relative to non-hybrid samples.
PVCF-Pipe (Population-VCF-Pipeline) is a generalized python pipeline for VCF file filtering and population genetics calculations from VCF-Tools. The pipeline allows user-customizable filtering and analysis options that performs intermediate calculations and averages for all populations represented in the VCF files, outputting all final metrics (Heterozygosity/Homozygosity, Pi, Fis, Tajima's D) into a single csv file for easy analyses of metrics between populations.
The GBIF Bioclim R Tookit (GBIF database and BioClimate Variables R Toolkit) comprises an R script template to source GBIF data and Bio-Climatic variables from WorldClim as well as functions that facilitate plotting of species distributions both across raster data and as density plots or histograms corresponding to the distribution of bioclimatic variables for GBIF samples that are geo-located with longitude and latitude data. Included are functions to break sample distributions based on intervals of geographic (i.e. longitude, latitude, or grids) or other input numeric ranges (i.e. elevation, other climate variables).
Feedback? Get In Touch!
We are continually working on improving our resources and developing new tools. Let us know how we can improve our tools or what new tools would benefit your bioinformatics needs!
email: contact@endemicbio.info