1. Polyploidy has appeared in almost every ancestral plant lineage, and in extant species, occurs frequently. When present, polyploidy presents problems for genetic data analysis, which are caused by both genotypic ambiguities and double‐reduction.
2. To address these problems, we developed a new software package, polygene, which enables the estimation of genotypic frequencies for a number of polysomic inheritance models. Specifically, polygene obtains posterior probabilities for genotypes hidden within allelic phenotypes.
3. Comprehensive modes of genetic analyses are provided by polygene, which include genetic diversity analysis, tests for allelic phenotypic or genotypic distributions, linkage disequilibrium and genetic differentiation, genetic distance analysis, principal coordinates analysis, hierarchical clustering analysis, individual inbreeding coefficient estimation, individual heterozygosity index estimation, population assignment, pairwise relatedness estimation, parentage analysis, analysis of molecular variance and Bayesian clustering.
4. polygene enables easy and convenient allelic phenotype‐ or genotype‐based analysis for both autopolyploids and diploids. polygene will thus facilitate molecular ecology research involving autopolyploids.

中文翻译：

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多基因：基于等位基因表型的同源多倍体的群体遗传学分析

1. 多倍体已经出现在几乎所有祖先植物谱系中，并且在现存物种中也经常发生。当存在多倍体时，遗传基因分析就会出现问题，这是由于基因型歧义性和双重还原而引起的。
2. 为了解决这些问题，我们开发了一个新的软件包，多基因，这使得基因型频率估计一些polysomic继承模型。具体而言，多基因获得隐藏在等位基因表型内的基因型的后验概率。
3. 多基因提供全面的遗传分析模式，包括遗传多样性分析，等位基因表型或基因型分布测试，连锁不平衡和遗传分化，遗传距离分析，主坐标分析，层次聚类分析，个体近交系数估计，个体杂合度指数估计，总体分配，成对相关性估计，亲子关系分析，分子方差分析和贝叶斯聚类。
4. polygene可以轻松，便捷地对等倍体和二倍体进行基于等位基因表型或基因型的分析。因此，多基因将促进涉及同源多倍体的分子生态学研究。