58 lines
1.4 KiB
YAML
Executable File
58 lines
1.4 KiB
YAML
Executable File
# KaKs Analysis Skill Configuration
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skill:
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name: kaks
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version: "1.0.0"
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description: "Ka/Ks分析 - 非同义/同义替换率计算与选择压力分析"
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author: "bbav20311-team"
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input:
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cds_fasta1: null # 必需: 物种1 CDS FASTA文件
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cds_fasta2: null # 必需: 物种2 CDS FASTA文件
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ortholog_pairs: null # 必需: 同源基因对列表
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parameters:
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alignment:
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tool: muscle
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maxiters: 2 # MUSCLE最大迭代次数
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kaks:
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method: yn00 # yn00方法计算Ka/Ks
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genetic_code: 0 # 通用遗传密码
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codeml:
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models:
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- M0 # 单一比率模型
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- M1 # 近中性模型
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- M7 # beta分布模型
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- M8 # beta+omega模型
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ncat: 10 # M7/M8的类别数
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fix_omega: 0 # 是否固定omega值
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omega: 1.0 # 初始omega值
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divergence:
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neutral_rate: 7.08e-9 # 中性替换率 (替换/位点/年)
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generation_time: 1 # 世代时间(年)，用于植物
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cpu: 8
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output:
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format: ["csv", "png", "pdf", "txt"]
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report_template: "templates/report.md.j2"
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include_reproducibility: true
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plots:
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- kaks_distribution
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- ka_vs_ks_scatter
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dependencies:
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conda:
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channels:
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- bioconda
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- conda-forge
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packages:
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- muscle=5.1
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- pal2nal=14.1
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- paml=4.10.6
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- biopython=1.81
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- pandas=2.0.0
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- matplotlib=3.7.0
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- seaborn=0.12.0
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- numpy=1.24.0
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- scipy=1.10.0
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