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arcs

Scaffold genome sequence assemblies using 10x Genomics data

augustus

Augustus is an open source system for building and scoring statistical models designed to work with data sets that are too large to fit into memory

beagle-lib

(Unofficial fork of) A general purpose library for evaluating the likelihood of sequence evolution on trees

blastgraph

cafe

Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

canu

A single molecule sequence assembler for genomes large and small.

cdna_primer

Scripts for processing PacBio transcriptome (Iso-Seq) data

clari-te

comparative-annotation-toolkit

diamond

Accelerated BLAST compatible local sequence aligner.

easycodeml

flo

Same species annotation lift over pipeline.

galaxytools

Galaxy Tool wrappers

gatk

Official code repository for GATK versions 4 and up

gatk-protected

GATK Official Release Repository: contains the core MIT-licensed GATK framework, plus "protected" tools restricted to non-commercial use only

genome-scripts

Genome Scripts used in fungal comparative genomics

hamstrad

Heavily modified version of HaMStR (Ebersberger et al., 2009)

homblocks

HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching

hpcgridrunner.github.io

web documentation for HpcGridRunner

irys-scaffolding

scripts to parse IrysView output

kaks-calculator

Automatically exported from code.google.com/p/kaks-calculator

ltr-finder

Automatically exported from code.google.com/p/ltr-finder

maize_v4_te_annotation

scripts and intermediate files used to annotate TEs in Jiao et al.

marvel

The MARVEL assembler

mecat

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

notepad-plus-plus

Notepad++ official repository

orthograph

Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models

paraat

paraat2.0 code and files for creation of dockerfile

pasa_lite

Stepping away from MySQL

phenolyzer

phenotype-based prioritization of candidate genes for human diseases