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2018_geneconversion_pipeline

Scripts for genome alignment, SNP calling, and recombination identification.

2019primate

Contains scripts used in Edsall et al., 2019

2024_phylogenomics_workshop

2024 workshop on phylogenomics, organized by Evomics

3d_dna_pipe

a-genome-assebmly-and-annotation-pipeline

A pipeline for assembling and annotating vertebrate genomes using Illumina short reads, PacBio or Nanopore long reads and HiC data

abc-enhancer-gene-prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

ac_snp-gene_pairing

accelerator

A bioinformatics research workflow for identifying Human Accelerated Regions (HARs)

adaptiphy

This computational method has been published in BMC genomics as: "Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral"

agat

Another Gtf/Gff Analysis Toolkit

ageingincardiocondyla

Scripts and data used in manuscript entitled: "Gene co-expression network reveals individualised compensatory responses to ageing in old ant queens"

agora

Algorithm For Gene Order Reconstruction in Ancestors

akrup

AKRUP: ancestral karyotype reconstruction universal pipeline

al2prunedtree

Prunes a given newick tree file to keep only taxa present in a given sequence alignment (FASTA format)

alignmentprocessor

Prepares CDS fasta Alignments for use with several programs

amas

Calculate summary statistics and manipulate multiple sequence alignments

amp_alignment_process

A workflow and toolkit of perl scripts to manipulate multiple sequence alignments

ampril-genomes

scripts for the project of seven thaliana genomes assembly

an-introduction-to-biostatistics-using-r

Biostatistics - Why? What? How?

analysispipeline-ngs

ancestral_genome_reconstruction

Instruction and scripts for reconstructing ancestral genome from pairwise syntenic blocks using MLGO

anchorwave

sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation

angiosperm-karyotype-evolution

核型进化Angiosperm karyotype evolution

annie

annie = ANNotation Information Extractor

annotate-gff

Add annotations to a GFF file

annotation

Scripts used in the annotation of B10K genomes

annotationpipeline-evm_based-dclab

基因组结构注释

ape_meth_bin

Scripts to run permutation analysis of methylation levels in apes.

apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.

applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020