TASSEL 5 User Manual

Introduction

• User

  • Web Site

  • Contributors

  • Citations

  • Getting Started

  • Executing TASSEL

  • Open Source Code

  • Software Development Tools

  • Graphical Interface

  • Pipeline (Command Line Interface) Tassel Pipeline Tutorial

  • GBSv2 Pipeline

  • UNEAK Pipeline

  • Tassel Pan-genome Atlas (PanA) Pipeline

• Developer

  • Tassel JavaDoc

  • Creating Tassel 5 Self-Describing Plugins

  • Building Tassel from Source

  • Tassel 5 Logging

File Menu

• Open / Open As...

  • Hapmap

  • HDF5 (Hierarchical Data Format version 5)

  • VCF (Variant Call Format)

  • Plink

  • Projection Alignment

  • Phylip

  • FASTA

  • Numerical Data

    • Phenotype Format

    • Trait Format

    • Covariate Format

    • Marker Values as Numerical Co-variates

  • Square Numerical Matrix

  • Table Report

  • TOPM (Tags on Physical Map)

  • Data Frequently Asked Questions

• Save As...

• Set Preferences

Data Menu

• Sort Genotype File

• Synonymizer (Synonymize Taxa Names)

• Joins

  • Intersect Join

  • Union Join

• Merge Genotype Tables

• Separate

• Homozygous Genotype

• SetLowDepthGenosToMissing

• Transform Phenotype

• Numerical Genotype

• ABH Genotype

• Thin Sites By Position

• Create Hybrid Genotypes

• Geno Summary

Impute Menu

• FILLIN

• FSFHap Imputation

• Numerical Impute

Filter Menu

• Filter Genotype Table Sites

• Filter Genotype Table Taxa

• Traits

  Not Recommended

• Sites

• Site Names

• Taxa Names

• Taxa

Analysis Menu

• Diversity

  • Diversity

  • Linkage Disequilibrium

• Relatedness

  • Distance Matrix

  • Kinship

  • Cladogram

  • Pedigree Relationship Matrix

  • Combined A and G Relationship Matrix

  • MDS

  • PCA

  • Remove NaN from Distance Matrix

• Genotype / Phenotype Association

  • GLM (General Linear Model)

  • MLM (Mixed Linear Model)

  • Weighted MLM (Mixed Linear Model)

  • Genomic Selection

  • Stepwise

  • Fast Association

  • VCAP Scan

Results Menu

• Table

• Archaeopteryx Tree

• LD Plot

• Chart

• QQ Plot

• Manhattan Plot

GBSv2 Menu

GBS Menu

Help Menu

• Help Manual

• About

• Show Memory

• Logging

Tutorial

• Tassel Youtube Tutorials

Appendix

• Nucleotide Codes (Derived from IUPAC)

• Depth Encodings

• TASSEL Tutorial Data sets

• References