pmckenz1
Ph.D. student, evolutionary biology. Genomics of gene flow and speciation in flowering plants
Harvard UniversityBoston, MA
Pinned Repositories
10-python-analysis2
11-plotting
GEOL_590
Class repository
intro-ml
Inference of phylogeny and introgression from genomic data, using machine learning models
ipcoal
Simulation package for getting gene tree distributions and loci / SNPs from input tree topologies and migration / Ne scenarios. Wraps around msprime.
mcpdiversity
Used to solve integer-programming problems encountered during my undergraduate thesis.
poolparty
Gamete-pooling method for recombination map inference
simcat
invariants and machine learning
smood
`smood` makes it simple to pull in observational data from GBIF and build species distribution maps. Go explore!
strange
Pop gen simulations
pmckenz1's Repositories
pmckenz1/ipcoal
Simulation package for getting gene tree distributions and loci / SNPs from input tree topologies and migration / Ne scenarios. Wraps around msprime.
pmckenz1/simcat
invariants and machine learning
pmckenz1/intro-ml
Inference of phylogeny and introgression from genomic data, using machine learning models
pmckenz1/smood
`smood` makes it simple to pull in observational data from GBIF and build species distribution maps. Go explore!
pmckenz1/10-python-analysis2
pmckenz1/11-plotting
pmckenz1/poolparty
Gamete-pooling method for recombination map inference
pmckenz1/strange
Pop gen simulations
pmckenz1/12-parallel-genomics
pmckenz1/6-scientific-python
Scientific tools for Python: Numpy, Scipy, Pandas
pmckenz1/7-remote-subprocess
SSH connections to HPC; remote jupyter; subprocess module
pmckenz1/assignment-1
pmckenz1/bef
Fun with species
pmckenz1/birdclips
Used for storing frames or short clips downloaded from a youtube livestream of birds. This is done automatically at consistent intervals each day.
pmckenz1/demography_sims
pmckenz1/flower_color_phenology
pmckenz1/gtinf
For now, simulating gene trees and sequences using msprime and seq-gen.
pmckenz1/hillside_mapping
Demo of making a Leaflet map for displaying EpiCollect5 data
pmckenz1/intralocus_recomb
pmckenz1/nn_sims
Fitting models to simulated data.
pmckenz1/piblog
In the name of independence from squarespace...
pmckenz1/pmckenz1.github.io
Personal website
pmckenz1/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers
aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)
pmckenz1/pyvolve
Python library to simulate evolutionary sequence data
pmckenz1/RevGadgets
Postprocessing gadgets for output generated by RevBayes
pmckenz1/stdpopsim
A library of standard simulation models for msprime
pmckenz1/toytree
A minimalist tree plotting library using toyplot graphs
pmckenz1/two_species_genealogy_probs
Adapted equations 14, 15, 16, and 17 of Rosenberg, "The Shapes of Neutral Gene Genealogies in Two Species: Probabilities of Monophyly, Paraphyly, and Polyphyly in a Coalescent Model", Evolution 2003 https://doi.org/10.1111/j.0014-3820.2003.tb00355.x
pmckenz1/waiting_times
Calculate waiting times to tree changes under the MSC with recombination (modeled with SMC')
pmckenz1/wordle_analysis
A fun weekend project.