Gene order can be used as an informative character to reconstruct phylogenetic relationships between species independently from the local information present in gene/protein sequences.PhyChro is a reconstruction method based on chromosomal rearrangements, applicable to a wide range of eukaryotic genomes with different gene contents and levels of synteny conservation. For each synteny breakpoint issued from pairwise genome comparisons, the algorithm defines two disjoint sets of genomes, named partial splits, respectively supporting the two block adjacencies defining the breakpoint. Considering all partial splits issued from all pairwise comparisons, a distance between two genomes is computed from the number of partial splits separating them. Tree reconstruction is achieved through a bottom-up approach by iteratively grouping sister genomes minimizing genome distances. PhyChro estimates branch lengths based on the number of synteny breakpoints and provides confidence scores for the branches.PhyChro performance is evaluated on two datasets of 13 vertebrates and 21 yeast genomes by using up to 130 000 and 179 000 breakpoints respectively, a scale of genomic markers that has been out of reach until now. PhyChro reconstructs very accurate tree topologies even at known problematic branching positions. Its robustness has been benchmarked for different synteny block reconstruction methods. On simulated data PhyChro reconstructs phylogenies perfectly in almost all cases, and shows the highest accuracy compared to other existing tools. PhyChro is very fast, reconstructing the vertebrate and yeast phylogenies in less than 15 min. AVAILABILITY PhyChro is freely available under the BSD license at http://www.lcqb.upmc.fr/phychro2/.

中文翻译：

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基于同线性块和基因邻接的系统发育重建。

基因顺序可以作为一种信息特征，独立于基因/蛋白质序列中存在的局部信息来重建物种之间的系统发育关系。PhyChro是一种基于染色体重排的重建方法，适用于具有不同基因内容的广泛真核基因组和同线性守恒水平。对于从成对基因组比较中发出的每个同线性断点，该算法定义了两个不相交的基因组集，称为部分分裂，分别支持定义断点的两个块邻接。考虑到所有成对比较产生的所有部分分裂，两个基因组之间的距离是根据分隔它们的部分分裂的数量来计算的。树重建是通过自下而上的方法通过迭代地分组姐妹基因组来最小化基因组距离来实现的。PhyChro 根据同线性断点的数量估计分支长度，并提供分支的置信度分数。 PhyChro 性能是在 13 个脊椎动物和 21 个酵母基因组的两个数据集上分别使用多达 130 000 个和 179 000 个断点（基因组标记的规模）进行评估到目前为止，这一直是遥不可及的。即使在已知有问题的分支位置，PhyChro 也能重建非常准确的树拓扑。其鲁棒性已针对不同的同线性块重建方法进行了基准测试。在模拟数据上，PhyChro 在几乎所有情况下都能完美地重建系统发育，并且与其他现有工具相比显示出最高的准确性。PhyChro 速度非常快，可在 15 分钟内重建脊椎动物和酵母系统发育。可用性 PhyChro 可根据 BSD 许可证免费提供，网址为：http://www.lcqb.upmc.fr/phychro2/。