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Script
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Output
OrthoFinder
Introduction

简介

基因序列之间的系统发育关系是比较生物学研究的基础。它为理解地球上生命的进化和多样性提供了框架，并能够在生物之间推断生物学知识。

OrthoFinder是一个快速，准确和全面的比较基因组学分析工具。它找到正交群(orthogroups) 和 直系同源(orthologs)，推断所有正交群的根基因树，并识别这些基因树中所有的基因复制事件。它还为被分析的物种推断出一个有根的物种树，并将基因复制事件从基因树映射到物种树的分支。OrthoFinder还提供了比较基因组分析的全面统计。

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本工作流采用 OrthoFinder 2.4.1版本，用户输入输入文件既可以得到结果。

输出工作流结果文件说明，请查看官方说明

更多信息可查看工具论文：

Emms, D.M. and Kelly, S. (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238

Emms, D.M. and Kelly, S. (2015) OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16:157

联系我们

该工具由国家基因库团队提供。如有任何问题或疑虑，请联系 CNGBdb@cngb.org

Script
Input
Task nameAttribute nameTypeDescription
*
      run_orthofinder
    fastasArray[File]
      Input fasta file list
    
*
      run_orthofinder.orthofinder
    search_threadsInt
      Number of parallel sequence search threads [Default = 16]
    
*
      run_orthofinder.orthofinder
    rooted_treeFile
      User-specified rooted species tree
    
*
      run_orthofinder.orthofinder
    mcl_inflationFloat
      MCL inflation parameter [Default = 1.5]
    
*
      run_orthofinder.orthofinder
    is_dnaBoolean
      Input is DNA sequences
    
*
      run_orthofinder.orthofinder
    is_SplitParaCladeBoolean
      Split paralogous clades below root of a HOG into separate HOGs
    
*
      run_orthofinder.orthofinder
    analysis_threadsInt
       Number of parallel analysis threads [Default = 1]
    
*
      run_orthofinder
    memoryString
      Number of memory running tasksnotice:1. The value range is 0.25-32 cores, in addition, 48 cores and 64 cores can be selected, and the CPU must be an integer multiple of 0.25 cores; 2. The memory value range is 1GB-512GB, and the memory must be an integer multiple of 1GB. 3. The CPU / memory ratio must be between 1:2 and 1:8
    
*
      run_orthofinder
    cpuString
      Number of CPU running tasks.notice:1. The value range is 0.25-32 cores, in addition, 48 cores and 64 cores can be selected, and the CPU must be an integer multiple of 0.25 cores; 2. The memory value range is 1GB-512GB, and the memory must be an integer multiple of 1GB. 3. The CPU / memory ratio must be between 1:2 and 1:8
    
Output
Task nameAttribute nameTypeDescription
*
      run_orthofinder
    StatisticsFile
      Comparative Genomics statistics file list.return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    DuplicationFile
      Gene Duplication Events file list.return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    Gene_TreesFile
      Gene Trees file list.return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    OrthogroupsFile
      orthogroups  file list.return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    OrthologuesFile
      Orthologues file list.return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    Orthogroup_SequencesFile
      FAST file list for each orthogroup.return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    Phylogenetic_OrthogroupsFile
       Phylogenetic Hierarchical Orthogroups.return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    Resolved_Gene_TreesFile
      A rooted phylogenetic tree inferred for each orthogroup with 4 or more sequences.return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    Single_Copy_Orthologue_SequencesFile
      Single_Copy_Orthologue_Sequences .return the output file to the column name of the corresponding table by this.xxx
    
*
      run_orthofinder
    Species_TreeFile
      Species_Tree.return the output file to the column name of the corresponding table by this.xxx