dportik
I enjoy developing practical tools for bioinformatics, genomics and evolutionary biology applications. Staff Bioinformatics Scientist @PacificBiosciences
@PacificBiosciencesSan Diego, CA
Pinned Repositories
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.
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.
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.
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.
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.
dportik's Repositories
dportik/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.
dportik/SuperCRUNCH
A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.
dportik/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.
dportik/Pandas-for-Population-Structure-Barplots
A jupyter notebook tutorial for making high-quality barplot figures from population structure analyses (Admixture, Structure) with Python & Pandas.
dportik/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.
dportik/MonoPhylo
A python tool for rapidly assessing the monophyly of user-defined groups in phylogenetic trees.
dportik/Academic-CV-vs-Industry-Resume
A 1:1 comparison of my academic CV and industry resume, with some tips on making an industry resume.
dportik/TaxonomyAlign
Taxonomy-guided multiple sequence alignment for difficult genes, including 12S and 16S mitochondrial rRNA.
dportik/admixture-wrapper
A tool to automate analyses in admixture, a program used for detecting population structure with SNP data.
dportik/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.
dportik/HiSSE_for_Afrobatrachia
Hidden state speciation and extinction analyses of sexual dichromatism in Afrobatrachian frogs.
dportik/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.
dportik/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.
dportik/SSDi-Calculator
A Python tool for calculating sexual size dimorphism indices from body size data. Performs permutation tests to determine statistically significant sexual dimorphism.
dportik/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.
dportik/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.
dportik/Coverage_Calculator
Script to help calculate coverage of a sample or contigs within a sample for sequence capture data sets.
dportik/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.
dportik/Duplicate_Counter
dportik/Exon_Coverage_Uniformity_Calculator
dportik/frog-body-size-evolution
dportik/gtdb_to_taxdump
Convert GTDB taxonomy to NCBI taxdump format
dportik/phyluce-genomes-to-supercrunch
Convert PHYLUCE genome-extracted UCE sequence data to GenBank style fasta labeling that is compatible with SuperCRUNCH.
dportik/Sensitivity_Calculator
dportik/Specificity_Calculator