Knowing phylogenetic relationships among species is fundamental for many studies in biology. An accurate phylogenetic tree underpins our understanding of the major transitions in evolution, such as the emergence of new body plans or metabolism, and is key to inferring the origin of new genes, detecting molecular adaptation, understanding morphological character evolution and reconstructing demographic changes in recently diverged species. Although data are ever more plentiful and powerful analysis methods are available, there remain many challenges to reliable tree building. Here, we discuss the major steps of phylogenetic analysis, including identification of orthologous genes or proteins, multiple sequence alignment, and choice of substitution models and inference methodologies. Understanding the different sources of errors and the strategies to mitigate them is essential for assembling an accurate tree of life.

中文翻译：

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在基因组时代的系统发育树建设。

了解物种之间的系统发育关系是许多生物学研究的基础。准确的系统树有助于我们了解进化中的主要转变，例如新的人体计划或新陈代谢的出现，并且是推断新基因的起源，检测分子适应性，了解形态特征演变和重建近期人口变化的关键分散的物种。尽管数据越来越丰富并且功能强大的分析方法可用，但是可靠的树构建仍然存在许多挑战。在这里，我们讨论了系统发育分析的主要步骤，包括直系同源基因或蛋白质的鉴定，多序列比对以及替代模型和推理方法的选择。