CrawlingSponge

JustinYoung's starred repositories

evals

Evals is a framework for evaluating LLMs and LLM systems, and an open-source registry of benchmarks.

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biopython

Official git repository for Biopython (originally converted from CVS)

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bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

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vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

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genomepy

genes and genomes at your fingertips

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tutorials

Tutorials on phylogenetic and phylogenomic inference

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miniprot

Align proteins to genomes with splicing and frameshift

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Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

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vgp-assembly

VGP repository for the genome assembly working group

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AdmixTools

Tools test whether admixture occurred and more

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GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.

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SynNet-Pipeline

Workflow for Building Microsynteny Networks

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HyDe

Hybridization detection using phylogenetic invariants

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G-PhoCS

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.

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