peterdfields

Fields_etal_2022_MBE

Angst_etal_2022_MolEcol

Scripts used in Angst et al. (2022)

parallel_snippets

stdpopsim

A library of standard population genetic models

3DFI

The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.

alphamissense

Angst_etal_2023_G3

Scripts used in Angst et al. (2023)

arabidopsis_numt-1

Analysis of Arabidopsis thaliana Chromosome 2 numt

awk_oneliners

Bash-Oneliner

A collection of handy Bash One-Liners and terminal tricks for data processing and Linux system maintenance.

bash_oneliners

Col-CEN

Resources for the Col-CEN reference genome assemblies

cs-nf-pipelines

The Jackson Laboratory Computational Sciences Nextflow based analysis pipelines

Daphnia_metacommunity

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

DeepMod2

DeepMod that works on Guppy or Tombo generated FAST5 files

degenotate

diploSHIC

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome

grenedalf

Toolkit for Analyzing Allele Frequencies of Pool-Sequenced Samples, e.g., in Evolve and Resequence experiments

homotools

latex-nihbiosketch

A LaTeX class implementing the new NIH Biographical Sketch Format

locator

deep learning prediction of geographic location from individual genome sequences

radeontop

redmask

Genome assembly soft-masking using Red (REpeat Detector)

rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments, including variant calling and more - relating to population genetics and insecticide resistance

Silene-Invasive-Data

transpecies_polymorphism_manuscript

TransPi

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly