Ctrl+F, and search the key words
Population genomics
Statistical Population Genomics(book)
linux
Coding language
Plot
Color
Colorbrewer2
data handling
trim fastq reads trimadap
SeqKit
FastQ processing fastp
Mapping
BWA
Maq (out-of-date)
stampy (out-of-date)
Bowtie (out-of-date)
Bowtie2
minimap
SAM/BAM flag explain
lastz
SNP/Indel calling
samtools
gatk
angsd
soapsnp
soapindel
pindel
dindel
Variant call format
about vcf format
vcftools
CNV calling
CNVnator
Genome STRiP
XHMM
ExomeCNV
CONTRA
ExomeCopy
ExomeDepth
CoNIFER
cn.mops - Mixture of Poissons for CNV detection in NGS data paper
cnvHiTSeq
CNVkit
PennCNV
Genotype phasing/ estimation of haplotypes
beagle
phase
fastphase
SHAPEIT
MACH
Genotype imputation
Phylogenetic tree
fasttree
RAxML
Phylip
PAUP* PAUP*
Phylogen Programs
compare two trees dendextend
Analysis tools
LD
IBD
Population Structure analysis
frappe
structure
admixture
ngsAdmix
ohana
PCA
Demographic history
dadi
psmc
msmc
smc++
treemix
fastsimcoal2
ChromoPainter/fineStructure/GLOBETROTTER
G-PhoCS
SLim
BEAST
Admix relatd:
ADMIXTOOLS here
ALDER
Seletive sweeps
sweep
ihs and xpehh
nSL
SweepFinder
SweeD
xp-clr
selscan
Composite of Multiple Signals (CMS), combines the signals from five different tests (ΔiHH, iHS, XP-EHH, FST and ΔDAF) to create a single test statistic CMS2.0 SabetiLab
Transcriptome
Trinity
velvet
Tophat
cufflinks
HISAT2
WGCNA (a R package for weighted correlation network analysis)
Network plot: Cytoscape
Iso-seq analysis of (alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts
(NAT), and circular RNAs (circRNAs) ) PRAPI
Database
DDBJ
ENA
NCBI
ensembl
ensembl plant
KEGG
reactome
GO
Plant transcription factor database (PlantTFDB)
Human Phenotype Ontology
GSA, Genome sequence archive of Beijing Institutes of Genomics(BIG)
水稻rice 3k rice
人human David Reich lab
GO/KEGG Enrichment
clusterProfiler
kaas
Gene Ontology
PANTHER
GORILLA
David
GWAS
FAST-LMM
GAPIT
EMMAX
NHGRI-EBI GWAS Catalog
GWAS Central
Odds Ratio（OR)and Risk Ratio(RR)
Metagenomics(MGWAS)
RAD-seq
SNP annotation
Gene annotation
EVidenceModeler(EVM)
DAVID
Gene2Function
Gene Structure Display Server, GSDS2
Plastome annotation (chloroplast genome)
bed annotation
Genomic search(bed file search/ranks the significance), GIGGLE Nature Method
Protein functional effects
PolyPhen-2
Protein-Protein Interaction Networks (STRING) 基因结构画图展示
Tools
Primer3 here
TMHMM (domain prediction)
Wego
Species & general Chinese name
tree of life
制作流程图 here
Venn diagram 维恩图: VennPainter Venny2.1
draw a plot like this weblogo
Understanding genome variation (BEDTOOLS, GEMINI, LUMPY, VCFANNO, PEDAGREE, and GQT)QuinlanLab
Cancer related
The Cancer Genome Atlas(TCGA) pan-cancer anlysis here
International Cancer Genome Consortium (ICGC)
National Cancer Institute (NCI)
National Comprehensive Cancer Network (NCCN), including NCCN guidelines for clinical application
ctDNA analysis(MutScan, GeneFuse, cfDNAPattern) HaploX
Disease
CDC Public Health Genomics Knowledge Base
疾病位点打分相关 M-CAP M-CAP online REVEL
ClinVar
dbNSFP
HGMD, Human Gene Mutation Database
SwissVar
MalaCards, The human disease database
evolution
UC berkeley, Understanding Evolution
tiktaalik roseae 你身体里的鱼 Your inner fish
Mouse Phenotype
mouse gene knockout and Phenotype
查基因功能网站：
Understanding genetics
Ask a Geneticists: The Tech Musemu of Innovation网站上的遗传学答页面，由斯坦福大学相关背景的志愿者撰写通俗易懂的回复。帮助理解遗传原理，包括遗传的过程、对基因检测中遗传病风险的理解等等。
Knockout mouse project
UCDavis KOMP
Contact
