Supplementary phylogenetic data for Rouïl et. al. 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"

Supplementary phylogenetic data for Rouïl et. al. 2020 "The protector within: Comparative genomics of APSE phages across aphids reveals rampant recombination and diverse toxin arsenals"

The data set consists of the following sub-directories:

1) "APSE_conserved_proteins_alns": Single-copy conserved genes codon sequences and alignments in FASTA format.

2) "APSE_phylogeny": Files used for APSE phylogenetic and recombination analyses.

3) "APSE_reannotations": GenBank-formatted files of the assemblies and re-annotations of APSE phages. Newly-sequenced phages deposited at the European nucleotide Archive are also included. ***New in this version***

4) "APSE_toxin_lyzozyme": Files used for APSE toxin-cassette and lyzozyme-related gene phylogenies.

5) "Arsenophonus_PHASTER": PHASTER phage annotation output files organised by organisim and contig/scaffold.

6) "Hamiltonella_drafts": Newly-sequenced low-coverage draft Hamiltonella genomes in FASTA format.

7) "Hamiltonella_phylogeny": files used for Hamiltonella phylogenetic analysis.

See enclosed README.txt file for more details.

* ver. 1.1.1: Updated annotations for APSE genomes including inteins missing in previous annotation files.

本数据集为Rouïl等人2020年发表的论文《体内防御者：蚜虫体内APSE噬菌体（APSE phages）比较基因组学揭示广泛重组与多样毒素库》的补充系统发育数据。

本数据集包含以下子目录：
1) "APSE_conserved_proteins_alns"：包含单拷贝保守基因的密码子序列及FASTA（FASTA）格式的比对文件。
2) "APSE_phylogeny"：用于APSE噬菌体系统发育与重组分析的文件。
3) "APSE_reannotations"：APSE噬菌体组装与重新注释的GenBank（GenBank）格式文件，同时包含已提交至欧洲核苷酸档案馆（European Nucleotide Archive）的新测序噬菌体。**本版本新增内容**
4) "APSE_toxin_lyzozyme"：用于APSE毒素盒与溶菌酶相关基因系统发育分析的文件。
5) "Arsenophonus_PHASTER"：按杀雄菌属（Arsenophonus）生物体与重叠群（contig）/支架（scaffold）分类的PHASTER（PHASTER）噬菌体注释输出文件。
6) "Hamiltonella_drafts"：FASTA（FASTA）格式的新测序低覆盖度汉密尔顿氏菌属（Hamiltonella）基因组草图。
7) "Hamiltonella_phylogeny"：用于汉密尔顿氏菌属系统发育分析的文件。

详细信息请参阅随附的README.txt文件。

* 版本1.1.1：更新了APSE基因组的注释内容，补充了此前注释文件中缺失的内含肽（inteins）。