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academic-cv-vs-industry-resume

A 1:1 comparison of my academic CV and industry resume, with some tips on making an industry resume.

admixture-wrapper

A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.

alignment_assessment

A tool for summarizing and visualizing metrics for sequence alignment files in phylip format. Designed to execute on a directory containing up to several thousand phylip files.

alignment_refiner

A script to filter phylip alignments by minimum bp length, missing data across individual sequence or whole alignment, with subsequent trimming function to reduce missing data.

convert-fasta-alignments-to-structure-format

Convert a set of phased alignment fasta files into a Structure input file. Intended to work with seq-capture and ddRADseq datasets.

coverage_calculator

Script to help calculate coverage of a sample or contigs within a sample for sequence capture data sets.

dadi_pipeline

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.

duplicate_counter

exon_coverage_uniformity_calculator

frog-body-size-evolution

gtdb_to_taxdump

Convert GTDB taxonomy to NCBI taxdump format

hisse_for_afrobatrachia

Hidden state speciation and extinction analyses of sexual dichromatism in Afrobatrachian frogs.

lrsw-taxonomic-profiling-tutorial

Perform taxonomic profiling analyses for long-read shotgun metagenomic datasets. Developed for the Long Read Sequencing Workshop 2022 at the Jackson Laboratory.

moments_pipeline

An accessible and flexible tool for fitting demographic models with moments using custom or published models (available here) and conducting goodness of fit tests.

monophylo

A python tool for rapidly assessing the monophyly of user-defined groups in phylogenetic trees.

pandas-for-population-structure-barplots

A jupyter notebook tutorial for making high-quality barplot figures from population structure analyses (Admixture, Structure) with Python & Pandas.

phylo_wrapper_scripts

Scripts to help automate various phylogenetic or phylogeography programs (Admixture, RAxML, CLUMPP + DISTRUCT). Also includes a script for replacing sample or taxon names in input files.

phylogenetic_tree_tools

Scripts for pruning taxa from tree files, performing Robinson-Foulds comparisons, and calculating node-support indices. All intended for a directory of tree files, rather than a single tree.

phyluce-genomes-to-supercrunch

Convert PHYLUCE genome-extracted UCE sequence data to GenBank style fasta labeling that is compatible with SuperCRUNCH.

sensitivity_calculator

specificity_calculator

ssdi-calculator

A Python tool for calculating sexual size dimorphism indices from body size data. Performs permutation tests to determine statistically significant sexual dimorphism.

stacks_pipeline

An automated workflow for processing ddRADseq data using Stacks v2.4. Starts with sequencer files, and ends with various input files for phylogenetic/phylogeography programs.

supercrunch

A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.

taxonomyalign

Taxonomy-guided multiple sequence alignment for difficult genes, including 12S and 16S mitochondrial rRNA.