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admixtools

Tools test whether admixture occurred and more

alan

Alignment viewer for linux terminal

anacapa

#### Written by Emily Curd ([email protected]), Jesse Gomer ([email protected]), Gaurav Kandlikar ([email protected]), Zack Gold ([email protected]), Max Ogden ([email protected]), Lenore Pipes ([email protected])and Baochen Shi ([email protected]). Assistance was provided by Rachel Meyer ([email protected]).

antcaller

SNP calling and genotyping for damaged DNA

astral

Accurate Species TRee ALgorithm

augustus

Genome annotation with AUGUSTUS

bcftools

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

beagle-lib

general purpose library for evaluating the likelihood of sequence evolution on trees

chrom-compare

gatk

Official code repository for GATK versions 4 and up

gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

gffutils

Convert, explore, and manipulate GFF and GTF files (used in bioinformatics) using a sqlite-based approach

grenepipe

Snakemake pipeline for variant calling from raw sequences

mapping-iterative-assembler

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mtannotate

Java program to transfer DNA annotations from a GenBank file to a FASTA sequence, intended for closely related mitochondrial genomes.

ngsld

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

north-american-ice-sheets

History of ice sheets and ice caps from the Last Glacial Maximum to present in North America, as produced by Dyke et al. (2003) and Dyke (2004)

paper-zhang2014

Source code from Zhang et al., (2014) Genomic data of avian phylogenomics project. GigaScience 3:26

partitionfinder

PartitionFinder discovers optimal partitioning schemes for DNA sequences.

popgen-notes

Population genetics notes

pophistory-tutorial

Tutorial on using popular tools for learning about population history

population_genomics_scripts

Scripts of population genomics analysis

pyule

CLI tool for simple calculations of rates and tree heights and lengths under Yule processes.

raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible

sea-cow

This repository includes the pipeline and commands which will useful for the paleogenome analysis

seqprep2

Tool for stripping adaptors and/or merging paired reads with overlap into single reads.

simpred

SNV impact predictor

snpeff

standard-raxml