Bioinformatics

Contributors: Xinshuai Qi

Genome Assembly

  • raw reads clean

  • De novo Assembly

    • Trinity

    • Velvet

  • Reference-based Assembly

    • Samtools

    • VCFtools

    • BCFtools

Genome Evolution and Genomics

  • OrthoFinder

  • Circos

  • SnpEff

  • Gene Ontology

  • LeafJ

Phylogenetics

  • RAxML

  • PAML

  • BEAST

  • TreeMix

Population Genetics and phylogeography

  • STRUCTURE

  • PCA and smartPCA

  • Provean

  • BadMutation

  • HAPMIX

  • ∂a∂i

  • DIY-ABC

  • fastSimCoal

  • SLiM2

  • TCS

  • Ecological Niche Modeling

    • WorldClim

RNASeq

  • TopHat

  • WGCNA

  • Cufflinks

Quantitative Genetics and GWAS

  • PLink

  • R/qtl

Long-read sequencing (PacBio and MinION)