Package: famCircle
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：
前期处理序列比对、共线性扫描、ks计算
ks展示
全基因组 ks展示
block ks展示
circle全基因组共线性展示
line局部共线性绘制
hmmer 隐马尔可夫模型搜索筛选
screen tandem数量分部
断开处：
pfam结构域筛选#http://pfam.xfam.org/α/β筛选#http://cb.csail.mit.edu/cb/paircoil2/主程序选择：
inner
typing 数据格式化
inner绘图
outer
typing 数据格式化
outer绘图
part局部tandem绘制配置文件解释总体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)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)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# 初筛阈值
e_value2 = value2# 复筛阈值结构域筛选α/β筛选结构域分布情况run screen
domainpath = domain file path
lens = lens file
gff = gff file
chrolist = Genome name
series = 25# 串联数
outpath = out file path文件格式化run typing
domainpath = domain file# 文件路径
domainlist = Genome name# 文件名列表
position = inner/outer# 目标程序格式
savefile = out file# 保存文件内卷型的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)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)[circle]
lens = lens file
gff = gff file
species_list = Genome name
ks = ks file
genepairs = genepairs file
block = 6
radius = 0.45
savefile = save file (*.png, *.pdf)[circle_all]
lens = lens file
gff = gff file
species_list = Genome name
blockfile = block file
radius = 0.3
savefile = save file (*.png, *.pdf)[hmmer]
pep = pep file
cds = cds file
hmmmoldpath = hmm file
format_conversion = Fales
comparison = clustal
e_value1 = value1
e_value2 = value2[inner]
lens = lens file
gff = gff file
chrolist = Genome name
ks = ks file
genefamily = famliy file
Ks_concern = 0,1.5
radius = 0.3
space = 0.005
clusters = True
peripheral = False
savecsv = outer file (.csv)
savefile = save file (.png, *.pdf)[Ks]
cds_file = 	cds file
pep_file = 	pep file
align_software = muscle
pairs_file = gene pairs file
ks_file = ks result[Ks_allocation]
ks = ks file
species_list = specise name
area = 0,2.5
model = YN00/NG86
savefile = save file (*.png, *.pdf)[Ks_block]
species_list = specise name
ks = ks file
area = 0,2.5
model = YN00/NG86
blockfile = block file
blocklength = 6
pvalue = 1e-5
savecsv = save csv
savefile = save file (*.png, *.pdf)[line]
pairs_file = pairs file
gff1 =  gff1 file
gff2 =  gff2 file
lens1 = lens1 file
lens2 = lens2 file
chr1_name =  chr1 name
chr2_name =  chr2 name
savefile = savefile(.png,.pdf)[outer]
lens = lens file
gff = gff file
chrolist = Genome name
ks = ks file
genefamily = famliy file
Ks_concern = 0,0.15
radius = 0.3
space = 0.005
clusters = True
peripheral = False
savecsv = outer file (.csv)
savefile = save file (.png, *.pdf)[part]
lens = lens file
gff = gff file
chrolist = Genome name
ks = ks file
genefamily = famliy file
Ks_concern = 0,1.5
radius = 0.3
space = 0.005
clusters = True
peripheral = False
savecsv = outer file (.csv)
savefile = save file (.png, *.pdf)[screen]
domainpath = domain file
lens = lens file
gff = gff file
chrolist = Genome name
series = 25
outpath = out file[typing]
domainpath = domain file
domainlist = Genome name
savefile = out file