Computational tools from various research groups

DNA Sequence Assembly & Analysis

ANGSD
ANGSD-wrapper
bamtools
bcftools
bedtools
bioawk
Bowtie 2
BWA
fastPHASE and PHASE
Genome Analysis Toolkit (GATK)
libsequence
Novoalign
Picard
PolyPhred
SAMtools
Scythe
seqqs
seqtk
VCFtools

Genetic Assignment

ADMIXTURE
CLUMPP
distruct
infocalc
InStruct
SCAT
Structure
Structurama
TESS

Genotyping & SNP Data

Alchemy

Marker & QTL Analyses

Eva Chan's R Scripts
hierfstat
LDHeatmap
plink
R/QTL

Simulation Tools

fwdpp
macs
ms
msms
SFS_CODE