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Gene finding pipeline for selenoprotein and selenocysteine machinery

Python 3 2 Updated Nov 22, 2024
C++ 18 1 Updated Jan 11, 2024

Fast implementation of the neighbour-joining phylogenetic inference method

C 21 5 Updated May 23, 2020

scripts to calculate and plot concordance vectors

R 1 Updated Jul 24, 2024

GONE: Scripts, programs and an example data set

C 44 3 Updated Dec 31, 2023

VCF2Dis: A new simple and efficient software to calculate p-distance matrix and construct population phylogeny based Variant Call Format

C++ 84 19 Updated Feb 3, 2025

Pipeline to calculate de novo mutation rates from parent-offspring trios

Ruby 5 1 Updated Jan 23, 2025

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

Python 77 33 Updated Jan 31, 2025

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

C 34 4 Updated Apr 27, 2021

oxford dot plots

Python 144 10 Updated Jan 23, 2025

Automated pipeline for running CoalHMM

Python 12 2 Updated Dec 4, 2023

mapping pipeline for ancient DNA

Python 27 3 Updated Dec 13, 2024

Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file

Python 47 8 Updated Oct 7, 2024

A Nextflow workflow to generate lift over files for any pair of genomes

Nextflow 56 10 Updated Feb 12, 2025

HemTools: a collection of NGS pipelines and bioinformatic analyses

Python 68 21 Updated Feb 17, 2025

Same species annotation lift over pipeline.

Ruby 96 28 Updated Jul 21, 2023

An accurate GFF3/GTF lift over pipeline

Python 466 56 Updated Aug 1, 2023

Calculate summary statistics and manipulate multiple sequence alignments

Python 78 14 Updated Feb 1, 2024

GenMap - Fast and Exact Computation of Genome Mappability

C++ 104 18 Updated Jun 20, 2024

Recombination Landscape Estimation using Recurrent Neural Networks

Python 53 12 Updated Jan 27, 2025

A phylogeny dating method using least-squares algorithms and criteria

C++ 25 6 Updated Oct 25, 2024

Download FASTQ files from SRA or ENA repositories.

Python 303 24 Updated Oct 20, 2024

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

C++ 2,010 334 Updated Nov 28, 2024

Fast and frugal disk based k-mer counter

C++ 284 73 Updated Nov 29, 2024

A fast multi-threaded k-mer counter

C++ 487 137 Updated Mar 20, 2024
Shell 1 Updated Jul 4, 2022

Tools and Utilities for msmc and msmc2

Python 47 17 Updated Aug 14, 2023

MSMC2 Scripts

Shell 23 4 Updated Mar 7, 2024

A pipeline to generate a phylogenetic tree from huge SNP data

Shell 86 38 Updated Dec 30, 2023

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

C++ 267 61 Updated Feb 19, 2025
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