Difference between revisions of "TASSEL"
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:Genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|tassel}} |{{#vardefine:url|http://www.maizegenetics.ne...") |
|||
| (4 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|tassel}} | |{{#vardefine:app|tassel}} | ||
| Line 21: | Line 21: | ||
relationship between phenotypes and genotypes1. TASSEL has functionality for association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. TASSEL development has been led by a group focused on maize genetics and genomics, and for these reasons that software has design and computational optimizations that account for the biology found in many plants and breeding situations. Compared to human genetics, many crops are highly diverse both at the nucleotide level and structural variations (10-50X greater than humans), inbreeding is common, large families are common, and whole genome prediction is being applied daily to real world problems. These biological differences lead to some different optimizations that are of use to many biological systems outside of crops. | relationship between phenotypes and genotypes1. TASSEL has functionality for association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. TASSEL development has been led by a group focused on maize genetics and genomics, and for these reasons that software has design and computational optimizations that account for the biology found in many plants and breeding situations. Compared to human genetics, many crops are highly diverse both at the nucleotide level and structural variations (10-50X greater than humans), inbreeding is common, large families are common, and whole genome prediction is being applied daily to real world problems. These biological differences lead to some different optimizations that are of use to many biological systems outside of crops. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
| − | |||
| − | < | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 16:13, 22 August 2022
Description
TASSEL stands for Trait Analysis by aSSociation, Evolution and Linkage. Its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes1. TASSEL has functionality for association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization. TASSEL development has been led by a group focused on maize genetics and genomics, and for these reasons that software has design and computational optimizations that account for the biology found in many plants and breeding situations. Compared to human genetics, many crops are highly diverse both at the nucleotide level and structural variations (10-50X greater than humans), inbreeding is common, large families are common, and whole genome prediction is being applied daily to real world problems. These biological differences lead to some different optimizations that are of use to many biological systems outside of crops.
Environment Modules
Run module spider tassel to find out what environment modules are available for this application.
System Variables
- HPC_TASSEL_DIR - installation directory