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README.md

famCircle 基因家族分析,tandem可视化分析

分析流程

基因组下载以及处理 路线1: ks展示 hmmer搜索筛选 断开处: pfam结构域筛选 α/β筛选 主程序选择: inner outer 路线2: blast、共线性文件筛选 主程序选择: inner outer

总体ks分布可视化

run ks ks = ks file vertical = False bins = 100 model = YN00/NG86 savefile = save file (*.png, *.pdf)

基因块ks分布可视化

run Ks_allocation ks = ks file area = 0,2 vertical = False model = YN00/NG86 blockfile = block file blocklength = 6 pvalue = 0.05 savefile = save file (*.png, *.pdf)

结构域分布情况

run screen domainpath = domain file lens = lens file gff = gff file chrolist = Genome name series = 25 outpath = out file

基因家族查找

run hmmer pep = pep file# 蛋白质文件 hmmmoldpath = hmm file# 模型地址 format_conversion = Fales# 格式转换 comparison = muscle/clustal# 比对软件 e_value1 = value1 e_value2 = value2

结构域筛选

α/β筛选

内卷型的tandem可视化

run inner lens = lens file gff = gff file chrolist = Genome name ks = ks file genefamily = famliy file Ks_concern = 0.1,0.2,1.4,1.5# ks分割参数可调 bridge = 0.05# 最远连接 radius = 0.3 peripheral = False savecsv = outer file (.csv) savefile = save file (.png, *.pdf)

共线性可视化

run circle lens = lens file gff = gff file chrolist = Genome name ks = ks file genepairs = genepairs file peripheral = False block = 6 Ks_concern = 0,0.15 bridge = 1 radius = 0.3 savefile = save file (*.png, *.pdf)

放射型的tandem可视化

run outer lens = lens file gff = gff file chrolist = Genome name ks = ks file genepairs = genepairs file Ks_concern = 0,0.15# ks分割参数可调 series = 25# 串联数 clusters = None# 集团参数可调 peripheral = False bridge = 1# 跨区域连线参数可调 radius = 0.3 savecsv = outer file (.csv) savefile = save file (.png, *.pdf)

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