Daniel Portik's repositories
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.
SuperCRUNCH
A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.
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.
Pandas-for-Population-Structure-Barplots
A jupyter notebook tutorial for making high-quality barplot figures from population structure analyses (Admixture, Structure) with Python & Pandas.
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.
Academic-CV-vs-Industry-Resume
A 1:1 comparison of my academic CV and industry resume, with some tips on making an industry resume.
TaxonomyAlign
Taxonomy-guided multiple sequence alignment for difficult genes, including 12S and 16S mitochondrial rRNA.
admixture-wrapper
A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.
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.
HiSSE_for_Afrobatrachia
Hidden state speciation and extinction analyses of sexual dichromatism in Afrobatrachian frogs.
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.
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.
SSDi-Calculator
A Python tool for calculating sexual size dimorphism indices from body size data. Performs permutation tests to determine statistically significant sexual dimorphism.
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.
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.
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.
gtdb_to_taxdump
Convert GTDB taxonomy to NCBI taxdump format
phyluce-genomes-to-supercrunch
Convert PHYLUCE genome-extracted UCE sequence data to GenBank style fasta labeling that is compatible with SuperCRUNCH.