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posted on 2019-08-27, 15:56 authored by Marcelo MollinariMarcelo Mollinari, Antonio Augusto Franco GarciaSupplementary 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
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