Supplemental Material for Mollinari and Garcia, 2019

Supplementary Information for the manuscript: "Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models"

1. File S1: Algebraic simplifications for transition probabilities
2. File S2: Algorithm for obtaining lP and lQ given two genotypic indices
3. File S3: Example of usage of the two-point and multipoint procedures to infer the linkage phase configuration in both parents and estimate recombination fractions in a sequence of markers in high-level autopolyploids.
4. Figure S4: Haplotypes for simulation study 1 - Simulated haplotypes with 10 markers and three ploidy levels, namely autotetraploid (m = 4), autohexaploid (m = 6) and autooctaploid (m = 8).
5. Figure S5: Haplotypes for simulation study 2 - Simulated haplotypes with 200 markers and two ploidy levels, namely autotetraploid (m = 4) and autohexaploid (m = 6).
6. Figure S6: Boxplots of the average Euclidean distances between the estimated and simulated distance vectors for simulation study 2
7. Figure S7: Examples autotetraploid and autohexapoloid maps estimated from datasets with three quadrivalent formation rates: 0.00, 0.25 and 0.50
8. File S8: Summary of results from B2721 population map construction
9. Figure S9: Simulated haplotypes for comparison between polymapR and HMM-based method
10. File S10: Results of comparison between polymapR and HMM-based method