Cydrasil-v3-reference-alignment.phy

This is a curated alignment generated using SSU-Align 0.1.1 with default parameters and masked using the ssu-mask feature of SSU-Align with per-alignment calculated masks. The alignment was then manually examined in Geneious version 8 to remove duplicate aligned sequences, non-16S rRNA sequences, and alignment errors. Sequences that were poorly aligned (typically due to the unlabeled inclusion of the ITS and/or 23S regions) were trimmed and removed if their length fell below the 1100 base pair threshold. The alignment was generated using the FASTA file cydrasil-v3-sequence-list.fasta found within the Cydrasil 3.0 figshare project. This alignment file is in phylip format.

本数据集为经人工整理优化的序列比对结果，采用SSU-Align 0.1.1及默认参数生成，并通过SSU-Align的ssu-mask功能，结合针对各比对计算得到的掩码完成掩码处理。随后，研究人员在Geneious 8软件中手动核查该比对结果，移除重复的比对序列、非16S核糖体RNA（rRNA）序列以及比对错误序列。对于比对质量不佳的序列（通常因未标注的内转录间隔区（ITS）和/或23S核糖体RNA区域被误纳入所致），将对其进行序列修剪；若修剪后序列长度低于1100碱基对阈值，则直接移除该序列。本次比对基于Cydrasil 3.0 Figshare项目中提供的FASTA格式文件cydrasil-v3-sequence-list.fasta生成，该比对文件采用phylip格式存储。