Table 1 Comparison of some LD software platforms
From: LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs
LDA | JLIN | Haploview | LD2SNPing | |
|---|---|---|---|---|
Input file formats | txt | csv | ped, info, txt | xls, csv, txt, doc |
Output file formats | pdf, eps, png, txt | png, txt | jpg, txt | |
D, D', r2, P | ✓ | ✓ | ✓ | ✓ |
δ Q , ρ | ✓ | ✓ | ✓ | |
Hardy-Weinberg equilibrium | ✓ | ✓ | ✓ | ✓ |
Genotype/haplotype frequency | ✓ | ✓ | ✓ | |
Tag SNP mining by gene input | ✓ | |||
SNP information retrieval by rsID input | ✓ | |||
Enzyme mining for RFLP genotyping | ✓ | |||
Online retrieval of multiple SNPs for LD plot | ✓ | |||
2D distance | ✓ | ✓ | ✓ | |
2D graph visualization | ✓ | ✓ | ✓ | ✓ |
2D graph/text data output | ✓ | ✓ | ✓ | |
3D distance/graph visualization | ✓ |