Pipeline to build a large human reference panel, using publicly available genomes

Heuristic search algorithm for fitting qpGraph models

Heatmap-integrated Decision Tree Visualizations

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

Precision HLA typing from next-generation sequencing data

Resources for calling and describing the circulating lineages of SARS-CoV-2

Repository of code for the paper "The evolutionary history of Neandertal and Denisovan Y chromosomes" by Petr et al.

tools for visualizing spatial genealogies

likelihood calculations over a tree to support ancient DNA Y chr analysis and more

Course material for STAT 479: Machine Learning (FS 2019) taught by Sebastian Raschka at University Wisconsin-Madison

Pinpoints the mutation favored by selection

Dimensionality reduction in very large datasets using Siamese Networks

initial commit

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Yleaf software for human Y-chromosomal haplogroup inference from next generation sequencing data

Finds SNP sites from a multi-FASTA alignment file

Details on the data analysis for "New kinship and F_ST estimates reveal higher levels of differentiation in the global human population" by Ochoa and Storey

An R package to estimate the quality of imputation of genotypes.

a pipeline for reconciliation of phylogenetic histories within a bacterial pangenome

Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis

A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence

An algorithm for recovering haplotypes from metagenomes

C++ multi-dimensional labeled arrays and dataframe based on xtensor

Merged into Gifsicle!