Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny

Supplementary data for "Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny."<br>hamstrsearch_model_taxa.sh: Commands used to process translated transcriptomes and predicted proteins from genomes with the HaMStR orthology inference software.<br>HaMStR_v13_modelorganisms_concatenate_orthologs.sh: Script used to create single fasta files for each HaMStR orthogroup from "fa_dir" folders created by HaMStR.<br><br>Phylogenomic_workflow_data_and_script_used.zip:<br>The script orthology_script.sh contains the commands used to go from the output of HaMStR_v13_modelorganisms_concatenate_orthologs.sh to the results in the PhyloTreePruner "pruned" folder. The results of SCaFoS analysis are in /scafos/.<br>18S_rDNA_alignment.phy:Alignment corresponding to Figure S2.<br>Transcriptome_assemblies_and_translations.zip:Newly sequenced transcriptome assemblies generated using Trinity and translations generated using TransDecoder.<br>《优化自由生活线虫系统基因组学采样以提升高阶线虫系统发育分辨率》一文的补充数据 hamstrsearch_model_taxa.sh：该脚本借助HaMStR直系同源推断软件，处理转录组翻译产物与基因组预测得到的蛋白质序列 HaMStR_v13_modelorganisms_concatenate_orthologs.sh：该脚本用于从HaMStR生成的"fa_dir"文件夹中，为每个HaMStR直系同源基因群生成单一FASTA格式文件 Phylogenomic_workflow_data_and_script_used.zip：该压缩包内含的orthology_script.sh脚本，收录了从HaMStR_v13_modelorganisms_concatenate_orthologs.sh的输出结果，到PhyloTreePruner“修剪后”文件夹中最终结果的全部处理命令。SCaFoS分析的结果存储于/scafos/目录下 18S_rDNA_alignment.phy：对应补充图S2的序列比对文件 Transcriptome_assemblies_and_translations.zip：包含采用Trinity软件组装得到的新测序转录组，以及通过TransDecoder软件预测得到的蛋白质翻译产物