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allele-specific-expression

Pipeline to perform the allele-specific expression analysis (based on the work by Skelly et al. 2011)

angsd

Program for analysing NGS data.

aster

Accurate Species Tree EstimatoR series: a family of optimation algorithms for species tree inference implemented in C++ (including ASTRAL-Pro & Weighted ASTRAL)

cactus

Official home of genome aligner based upon notion of Cactus graphs

ckmedoidstreeclustering

A new fast method for building multiple consensus trees using k-medoids

comparative-annotation-toolkit

csa

Cyclic DNA Sequence Aligner

csavanalysis

This analysis aims to detect convergent single amino acid variants among species from polyphyletic clades

datasharing

The Leek group guide to data sharing

falseduplication

false duplication and false gene gain research for VGP assemblies.

friendsdontletfriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

fruf_v1_assembly

The genome assembly pipeline for Fulvetta ruficapilla.

gatk-docs

Documentation archive for GATK tools and workflows

gene-family-analysis

gotree

Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.

hotfoxes

Scripts for Rocha et al. 2023: "North-African fox genomes show signatures of repeated introgression and adaptation to life in deserts"

hqgr

The High Quality Reads Generator (HQGR) script is provided to implement second round of CCS for long amplicon HiFi sequencing.

hummingbird

kakapo

Scripts and code for Kākāpō genomic data

locsi-for-non-model-species

ma

The Modular Aligner and The Modular SV Caller

maftools

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

monotremegenome

Custom scripts for monotreme genome project

nam-genomes

Detailed bioinformatics scripts and methods used in the NAM genome paper.

paleomix

Pipelines and tools for the processing of ancient and modern HTS data.

phybin

Binning (Newick) Phylogenetic Trees by Topology

phykit

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

phylociraptor

rapid phylogenomic tree calculator - A highly customizable framework for reproducible phylogenomic inference

pixy

Software for painlessly estimating average nucleotide diversity within and between populations

polarizepigancestralalleles