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。
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:
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 name | Attribute name | Type | Description |
---|---|---|---|
* run_orthofinder | fastas | Array[File] | Input fasta file list |
run_orthofinder.orthofinder | search_threads | Int | Number of parallel sequence search threads [Default = 16] |
run_orthofinder.orthofinder | rooted_tree | File | User-specified rooted species tree |
run_orthofinder.orthofinder | mcl_inflation | Float | MCL inflation parameter [Default = 1.5] |
run_orthofinder.orthofinder | is_dna | Boolean | Input is DNA sequences |
run_orthofinder.orthofinder | is_SplitParaClade | Boolean | Split paralogous clades below root of a HOG into separate HOGs |
run_orthofinder.orthofinder | analysis_threads | Int | Number of parallel analysis threads [Default = 1] |
run_orthofinder | memory | String | 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 | cpu | String | 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 name | Attribute name | Type | Description |
---|---|---|---|
* run_orthofinder | Statistics | File | Comparative Genomics statistics file list.return the output file to the column name of the corresponding table by this.xxx |
* run_orthofinder | Duplication | File | Gene Duplication Events file list.return the output file to the column name of the corresponding table by this.xxx |
* run_orthofinder | Gene_Trees | File | Gene Trees file list.return the output file to the column name of the corresponding table by this.xxx |
* run_orthofinder | Orthogroups | File | orthogroups file list.return the output file to the column name of the corresponding table by this.xxx |
* run_orthofinder | Orthologues | File | Orthologues file list.return the output file to the column name of the corresponding table by this.xxx |
* run_orthofinder | Orthogroup_Sequences | File | FAST file list for each orthogroup.return the output file to the column name of the corresponding table by this.xxx |
* run_orthofinder | Phylogenetic_Orthogroups | File | Phylogenetic Hierarchical Orthogroups.return the output file to the column name of the corresponding table by this.xxx |
* run_orthofinder | Resolved_Gene_Trees | File | 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_Sequences | File | Single_Copy_Orthologue_Sequences .return the output file to the column name of the corresponding table by this.xxx |
* run_orthofinder | Species_Tree | File | Species_Tree.return the output file to the column name of the corresponding table by this.xxx |