1. File S1: Algebraic simplifications for transition probabilities

2. File S2: Algorithm for obtaining l_{P} and l_{Q} 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