NEO_ML_tree_codonPhyML

The maximum likelihood tree inferred from "NEO_alignment.fas", using CodonPhyML. We used the GY model with four categories of non-synonymous/synonymous substitution rate ratios drawn from the discrete gamma distribution, and codon frequencies were estimated from the data under the F3X4 model. The tree topology search was done using the NNI approach, and branch support was estimated using the SH-like aLRT method. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.本研究基于"NEO_alignment.fas"序列比对文件，通过CodonPhyML软件构建得到最大似然树（maximum likelihood tree）。本研究采用GY模型（GY model），将非同义/同义替换速率比按离散伽马分布划分为4个类别，并基于F3X4模型从序列数据中估算密码子频率。树拓扑结构搜索采用最近邻互换（NNI，Nearest Neighbor Interchange）方法，分支支持度通过类SH近似似然比检验（SH-like aLRT）方法进行估算。物种名称后的字母数字编码为4位字母的1KP转录组标识符、GenBank登录号，或两者兼具。