{"id":1365,"date":"2024-12-09T09:52:24","date_gmt":"2024-12-09T01:52:24","guid":{"rendered":"http:\/\/www.majunpeng.com\/?p=1365"},"modified":"2026-01-22T11:54:41","modified_gmt":"2026-01-22T03:54:41","slug":"%e5%85%a8%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%8a%a0%e5%80%8d%ef%bc%88wgd%ef%bc%89","status":"publish","type":"post","link":"http:\/\/www.majunpeng.com\/index.php\/2024\/12\/09\/%e5%85%a8%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%8a%a0%e5%80%8d%ef%bc%88wgd%ef%bc%89\/","title":{"rendered":"\u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08WGD\uff09"},"content":{"rendered":"\t\t
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WGDI: \u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08WGD\uff09<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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1.\u6570\u636e\u51c6\u5907\u548c\u9884\u5904\u7406<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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WGDI\u8981\u6c42\uff081\uff09\u57fa\u56e0\u7ec4\u6587\u4ef6\uff1b\uff082\uff09\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6\uff08gff\uff09\uff1b\uff083\uff09CDS\uff1b\uff084\uff09\u86cb\u767d\u5e8f\u5217<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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# WGDI \u5bf9\u57fa\u56e0\u7ec4\u6ce8\u91ca\u3001CDS\u548c\u86cb\u767d\u5e8f\u5217\u6587\u4ef6\u6709\u72ec\u7279\u7684\u683c\u5f0f\u548cID\u8981\u6c42\uff0c\u53ef\u4ee5\u901a\u8fc7\u4f5c\u8005\u7684\u811a\u672c\u6765\u8fdb\u884c\u8f6c\u6362\uff0c\u811a\u672c\u4e0b\u8f7d\u5730\u5740\uff0c<\/p>

python .\/Script\/getgff.py Genome.gff tmp_Genome.gff<\/p>

# Genome.gff\uff1a\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6<\/p>

# tmp_Genome.gff\uff1a\u8f6c\u6362\u7684\u4e2d\u95f4\u8fc7\u7a0b\u6587\u4ef6\uff0c\u540e\u7eed\u4f1a\u7528\u5230<\/p>

python ..\/Script\/gff_lens.py tmp_Genome.gff WGDI_Genome.gff Genome_length.txt<\/p>

# WGDI_Genome.gff\uff1aWGDI\u8981\u6c42\u7684\u7279\u5b9a\u683c\u5f0f\u7684\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6<\/p>

# Genome_length.txt\uff1a\u57fa\u56e0\u7ec4\u4fe1\u606f\u7edf\u8ba1\u7ed3\u679c\uff0c\u7edf\u8ba1\u4e86\u6bcf\u6761\u67d3\u8272\u4f53\u7684\u957f\u5ea6\u548c\u57fa\u56e0\u7684\u6570\u91cf<\/p>

python ..\/Script\/seq_newname.py WGDI_Genome.gff Genome_pep.fasta WGDI_Genome_pep.fasta<\/p>

# Genome_pep.fasta\uff1a\u86cb\u767d\u6587\u4ef6<\/p>

# WGDI_Genome_pep.fasta\uff1a\u6839\u636e\u65b0\u751f\u6210\u7684gff\u6587\u4ef6\uff0c\u91cd\u547d\u540d\u540e\u7684\u86cb\u767d\u6587\u4ef6<\/p>

python ..\/Script\/seq_newname.py WGDI_Genome.gff Genome_cds.fasta WGDI_Genome_cds.fasta<\/p>

# Genome_pep.fasta\uff1aCDS\u6587\u4ef6<\/p>

# WGDI_Genome_pep.fasta\uff1a\u6839\u636e\u65b0\u751f\u6210\u7684gff\u6587\u4ef6\uff0c\u91cd\u547d\u540d\u540e\u7684CDS\u6587\u4ef6<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2. \u8fd0\u884cWGDI<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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WGDI\u7684\u8fd0\u884c\u4e3a\u591a\u6a21\u5757\u5206\u6bb5\uff0c\u9700\u8981\u4f9d\u6b21\u8fdb\u884c\u5404\u4e2a\u6a21\u5757\u7684\u8fd0\u884c\u3002<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u8fd0\u884c Blast<\/p>

blastp -num_threads 150 -db Genome_pep.fasta -query Genome_pep.fasta -outfmt 6 -evalue 1e-5 -out Genme_blast.txt<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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2.1 Collinearity \u6a21\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u751f\u6210\u914d\u7f6e\u6587\u4ef6<\/p>

wgdi -icl \\? >> Collinearity.conf ###\u6b63\u5e38\u662fwgdi<\/span>\u00a0-icl<\/span>\u00a0?<\/span>\u00a0>><\/span> Collinearity.conf\uff0c\u4f46\u662f\u7531\u4e8e\uff1f\u9700\u8981\u8f6c\u8bd1\uff0c\u6240\u4ee5\u8981\u5728\u524d\u9762\u52a0\u4e00\u4e2a\\<\/span><\/p>

# Collinearity \u6a21\u5757\u914d\u7f6e\u6587\u4ef6<\/p>

[collinearity]
gff1 = gff1 file #\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6
gff2 = gff2 file #\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6
lens1 = lens1 file #\u57fa\u56e0\u7ec4\u7edf\u8ba1\u4fe1\u606f\u6587\u4ef6
lens2 = lens2 file #\u57fa\u56e0\u7ec4\u7edf\u8ba1\u4fe1\u606f\u6587\u4ef6
blast = blast file # Blast\u7ed3\u679c\u6587\u4ef6
blast_reverse = false
multiple = 1
process = 8
evalue = 1e-5
score = 100
grading = 50,40,25
mg = 40,40
pvalue = 0.2
repeat_number = 10
positon = order
savefile = Genome_collinearity.txt # \u8f93\u51fa\u7684\u7ed3\u679c\u6587\u4ef6<\/p>

# \u8fd0\u884c<\/p>

wgdi -icl Collinearity.conf<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2.2 Non-synonymous (Ka) and synonymous (Ks) \u6a21\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u751f\u6210\u914d\u7f6e\u6587\u4ef6<\/p>

wgdi -ks ? >> KaKs.conf<\/p>

# Non-synonymous (Ka) and synonymous (Ks) \u914d\u7f6e\u6587\u4ef6<\/p>

[ks]
cds_file = WGDI_Genome_cds.fasta # \u57fa\u56e0\u7ec4CDS\u6587\u4ef6
pep_file = WGDI_Genome_pep.fasta # \u57fa\u56e0\u7ec4\u86cb\u767d\u5e8f\u5217\u6587\u4ef6
align software = muscle
pairs_file = Genone_Collinearity.txt
ks_file = Genone_Ksks.txt # \u8f93\u51fa\u7ed3\u679c\u6587\u4ef6<\/p>

# \u8fd0\u884c<\/p>

wgdi -ks KaKs.conf<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2.3 BlockInfo \u6a21\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u751f\u6210\u914d\u7f6e\u6587\u4ef6<\/p>

wgdi -ks ? >> BlockInfo.conf<\/p>

# BlockInfo \u914d\u7f6e\u6587\u4ef6<\/p>

[blockinfo]
blast = Genome_blast.txt
gff1 = WGDI_Genome.gff
gff2 = WGDI_Genome.gff
lens1 = Genome_length.txt
lens2 = Genome_length.txt
collinearity = Genome_Collinearity.txt
score = 100
evalue = 1e-5
repeat_number = 10
position = order
ks = Genome_ks.txt
ks_col = ks_NG86
savefile = Genome_block.csv # \u8f93\u51fa\u7ed3\u679c\u6587\u4ef6<\/p>

# \u8fd0\u884c<\/p>

wgdi -bi BlockInfo.conf<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2.4 BlockKs \u6a21\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u751f\u6210\u914d\u7f6e\u6587\u4ef6<\/p>

wgdi -ks ? >> Blockks.conf<\/p>

# BlockInfo \u914d\u7f6e\u6587\u4ef6<\/p>

[blockks]
lens1 = Genome_length.txt
lens2 = Genome_length.txt
genome1_name = Genome.fasta # \u57fa\u56e0\u7ec4\u5e8f\u5217\u6587\u4ef6
genome2_name = Genome.fasta # \u57fa\u56e0\u7ec4\u5e8f\u5217\u6587\u4ef6
blockinfo = Genome_block.csv
pvalue = 0.05
tandem = true
tandem_length = 200
markersize = 1
area = 0,2
block_length = 5
figsize = 8,8
savefig = Genome_Blockks.pnf # \u8f93\u51fa\u7684\u7ed3\u679c\u6587\u4ef6<\/p>

# \u8fd0\u884c<\/p>

wgdi -bk Blockks.conf<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2.5 Kspeaks \u6a21\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u751f\u6210\u914d\u7f6e\u6587\u4ef6<\/p>

wgdi -ks ? >> KsPeaks.conf<\/p>

# \u914d\u7f6e\u6587\u4ef6<\/p>

[kspeaks]<\/p>

blockinfo = Genome_block.csv
pvalue = 0.2
tandem = true
block_ length = 5
ks_area = 0,10
multiple = 1
homo = -1,1
fontsize = 9
area = 0,3
figsize = 10,6.18
savefig = Genome_Kspeaks.png # Ks\u5206\u5e03\u56fe
savefile = Genome_Kspeaks.csv # \u8f93\u51fa\u7ed3\u679c\u6587\u4ef6<\/p>

# \u8fd0\u884c<\/p>

wgdi -kp KsPeaks.conf<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
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Ks\u5206\u5e03\u56fe<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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Ks\u5206\u5e03\u56fe\u53ef\u4ee5\u770b\u5230\u4e24\u4e2a\u660e\u663e\u7684\u5cf0\uff0cKs1\uff080.2\uff09\u548cKs2\uff081.2\uff09\u3002WGDI\u7684KsPeaks\u6a21\u5757\u4e00\u6b21\u53ea\u80fd\u62df\u5408\u4e00\u4e2a\u5cf0\u503c\uff0c\u6240\u4ee5\u6211\u4eec\u8981\u91cd\u65b0\u8fd0\u884cKspeaks\u6a21\u5757\uff0c\u5206\u522b\u8fd0\u884c\u4e24\u6b21\uff0c\u5f97\u52302\u4e2a\u7ed3\u679c\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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# Ks1 \u914d\u7f6e\u6587\u4ef6<\/p>

[kspeaks]<\/p>

blockinfo = Genome_block.csv
pvalue = 0.2
tandem = true
block_ length = 5
ks_area = 0,0.75
multiple = 1
homo = -1,1
fontsize = 9
area = 0,3
figsize = 10,6.18
savefig = Genome_Kspeaks_1.png # Ks1\u5206\u5e03\u56fe
savefile = Genome_Kspeaks_1.csv # Ks1\u8f93\u51fa\u7ed3\u679c\u6587\u4ef6<\/p>

# Ks1 \u914d\u7f6e\u6587\u4ef6<\/p>

[kspeaks]<\/p>

blockinfo = Genome_block.csv
pvalue = 0.2
tandem = true
block_ length = 5
ks_area = 0.75,2
multiple = 1
homo = -1,1
fontsize = 9
area = 0,3
figsize = 10,6.18
savefig = Genome_Kspeaks_2.png # Ks2 \u5206\u5e03\u56fe
savefile = Genome_Kspeaks_2.csv # Ks2 \u8f93\u51fa\u7ed3\u679c\u6587\u4ef6<\/p>

# \u8fd0\u884c<\/p>

wgdi -kp KsPeaks.conf<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2.6 PeakFit \u6a21\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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# \u751f\u6210\u914d\u7f6e\u6587\u4ef6<\/p>

wgdi -ks ? >> PeakFit.conf<\/p>

# \u914d\u7f6e\u6587\u4ef6<\/p>

[peaksfit]<\/p>

blockinfo = Genome_Kspeaks_1.csv
mode = median
bins_number = 200
ks_area = 0,10
fontsize = 9
area = 0,3
figsize = 10,6.18
savefig = Genome_PeakFit_1.png<\/p>

[peaksfit]<\/p>

blockinfo = Genome_Kspeaks_2.csv
mode = median
bins_number = 200
ks_area = 0,10
fontsize = 9
area = 0,3
figsize = 10,6.18
savefig = Genome_PeakFit_2.png<\/p>

# \u8fd0\u884c<\/p>

wgdi -pf PeakFit.conf<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
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\u8fd0\u884c\u6210\u529f\u540e\uff0c\u4f1a\u6253\u5370\u66f2\u7ebf\u62df\u5408\u7684\u4fe1\u606f\uff0c\u540e\u7eed\u7684KsFigture\u6a21\u5757\u4f1a\u7528\u5230<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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2.7 KsFigure \u6a21\u5757<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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KsFigure \u6a21\u5757\u8fd0\u884c\u9700\u8981\u4e00\u4e2aCSV\u683c\u5f0f\u7684\u8f93\u5165\u6587\u4ef6\uff0c\u683c\u5f0f\u5982\u4e0b\uff0c\u5982\u679c\u9700\u8981\u62df\u5408\u591a\u4e2a\u66f2\u7ebf\uff0c\u53ef\u4ee5\u4f9d\u6b21\u589e\u52a0\u884c\u6570\u3002<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t
\n\n\n\n\t\n\n\t\n\t\n\t\n\t
<\/th>color<\/th>linewidth<\/th>linestyle<\/th><\/th><\/th><\/th><\/th><\/th><\/th>\n<\/tr>\n<\/thead>\n
Chr_Chr<\/td>green<\/td>1<\/td>--<\/td>5.02<\/td>0.83<\/td>0.10<\/td>2.08<\/td>1.83<\/td>0.25<\/td>\n<\/tr>\n
<\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td>\n<\/tr>\n
<\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td>\n<\/tr>\n
<\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t

# \u751f\u6210\u914d\u7f6e\u6587\u4ef6<\/p>

wgdi -ks ? >> KsFigure.conf<\/p>

# \u914d\u7f6e\u6587\u4ef6<\/p>

[ksfigure]
ksfit = Genome_PeakFit.csv # PeakFit\u7684\u62df\u5408\u4fe1\u606f
labelfontsize = 15
legendfontsize = 15
xlabel = none
ylabel = none
title = none
area = 0,2
figsize = 10,6.18
shadow = true
savefig = Genome_Ks.png # Ks\u66f2\u7ebf\u62df\u5408\u7ed3\u679c<\/p>

# \u8fd0\u884c<\/p>

wgdi -kf KsFigure.conf<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

\n\t\t\t\t
\n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
\n\t\t\t\t
\n\t\t\t\t\t

3. \u5faa\u73af\u8fd0\u884c<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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3.1 \u7269\u79cd\u5185Ks<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t
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Diamond \u6784\u5efa\u7d22\u5f15<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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\n\t\t\t\t\t\t\t
\n\t\t\t
\n\t\t\t\t\n\t\t\t\t\tfor i in Oryza_sativa Olyra_latifolia Phyllostachys_edulis Guadua_angustifolia Dendrocalamus_latiflorus Bambusa_pervariabilis_Dendrocalamopsis_daii Bambusa_pervariabilis_Dendrocalamopsis_daii\ndo\ndiamond makedb --in ${i}.pep -d ${i}.pep\ndone<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-57b2954 elementor-widget elementor-widget-text-editor\" data-id=\"57b2954\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd0\u884cDiamond<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-fb97db7 elementor-widget elementor-widget-code-highlight\" data-id=\"fb97db7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>for i in Oryza_sativa Olyra_latifolia Phyllostachys_edulis Guadua_angustifolia Dendrocalamus_latiflorus\ndo\ndiamond blastp -q ${i}.pep -d ${i}.pep -o ${i}_${i}.blast -p 40\ndone<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-78ffd1f elementor-widget elementor-widget-text-editor\" data-id=\"78ffd1f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u6279\u91cf\u751f\u6210WGDI\u914d\u7f6e\u6587\u4ef6<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4694650 elementor-widget elementor-widget-text-editor\" data-id=\"4694650\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd0\u884cWGDI<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-0f5f192 elementor-widget elementor-widget-code-highlight\" data-id=\"0f5f192\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>for i in {Chrysanthemum_seticuspe,Chrysanthemum_indicum,Shidagonglao}\ndo            \necho \"\n[collinearity]\ngff1 = ${i}.gff  \ngff2 = ${i}.gff  \nlens1 = ${i}_length.txt\nlens2 = ${i}_length.txt\nblast = ${i}_${i}.blast\nblast_reverse = no\nmultiple = 1\nprocess = 50\nevalue = 1e-5\nscore = 100\ngrading = 50,40,25\nmg = 25,25\npvalue = 1\nrepeat_number = 10\npositon = order\nsavefile = ${i}_${i}.icl\n\n[ks]\ncds_file = Conbine.cds\npep_file = Conbine.pep\nalign_software = muscle\npairs_file = ${i}_${i}.icl\nks_file = ${i}_${i}.ks\n\n[blockinfo]\nblast = ${i}_${i}.blast\ngff1 = ${i}.gff\ngff2 = ${i}.gff\nlens1 = ${i}_length.txt\nlens2 = ${i}_length.txt\ncollinearity = ${i}_${i}.icl\nscore = 100\nevalue = 1e-5\nrepeat_number = 10\nposition = order\nks = ${i}_${i}.ks\nks_col = ks_NG86\nsavefile = ${i}_${i}_block.csv\n\n[kspeaks]\nblockinfo = ${i}_${i}_block.csv\npvalue = 0.2\ntandem = true\nblock_length = 5\nks_area = 0,10\nmultiple = 1\nhomo = -1,1\nfontsize = 9\narea = 0,3\nfigsize = 10,6.18\nsavefig = ${i}_${i}_Kspeaks.png\nsavefile = ${i}_${i}_Kspeaks.csv\n\n[peaksfit]\nblockinfo = ${i}_${i}_block.csv\nmode = median\nbins_number = 200\nks_area = 0,10\nfontsize = 9\narea = 0,3\nfigsize = 10,6.18\nshadow = true \nsavefig = ${i}_${i}_pf.png\" > ${i}.conf\ndone<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5fd95ff elementor-widget elementor-widget-code-highlight\" data-id=\"5fd95ff\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>for i in Oryza_sativa Olyra_latifolia Phyllostachys_edulis Guadua_angustifolia Dendrocalamus_latiflorus Bambusa_pervariabilis_Dendrocalamopsis_daii\ndo\nwgdi -icl ${i}.conf\nwgdi -ks ${i}.conf\nwgdi -bi ${i}.conf\nwgdi -kp ${i}.conf\ndone<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-82339e2 elementor-widget elementor-widget-heading\" data-id=\"82339e2\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">3.2 \u7269\u79cd\u95f4Ks<\/h2>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-9751340 elementor-widget elementor-widget-text-editor\" data-id=\"9751340\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd0\u884cDiamond<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6a0c590 elementor-widget elementor-widget-code-highlight\" data-id=\"6a0c590\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>for i in Phyllostachys_edulis Oryza_sativa Olyra_latifolia Melocanna_humilis Guadua_angustifolia Dendrocalamus_latiflorus \ndo\ndiamond blastp -q ${i}.pep -d Bambusa_pervariabilis_Dendrocalamopsis_daii.pep -o ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.blast  -p 40\ndone<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-e0b9611 elementor-widget elementor-widget-text-editor\" data-id=\"e0b9611\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u6279\u91cf\u751f\u6210WGDI\u914d\u7f6e\u6587\u4ef6<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-0e84dd3 elementor-widget elementor-widget-text-editor\" data-id=\"0e84dd3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>\u8fd0\u884cWGDI<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1e2a4cd elementor-widget elementor-widget-code-highlight\" data-id=\"1e2a4cd\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>for i in Phyllostachys_edulis Oryza_sativa Olyra_latifolia Melocanna_humilis Guadua_angustifolia Dendrocalamus_latiflorus\ndo\necho \"\n[collinearity]\ngff1 = ${i}.gff\ngff2 = Bambusa_pervariabilis_Dendrocalamopsis_daii.gff\nlens1 = ${i}_length.txt\nlens2 = Bambusa_pervariabilis_Dendrocalamopsis_daii_length.txt\nblast = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.blast\nblast_reverse = false\nmultiple = 1\nprocess = 50\nevalue = 1e-5\nscore = 100\ngrading = 50,40,25\nmg = 25,25\npvalue = 1\nrepeat_number = 10\npositon = order\nsavefile = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.icl\n\n[ks]\ncds_file = Conbine.cds\npep_file = Conbine.pep\nalign_software = muscle\npairs_file = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.icl\nks_file = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.ks\n\n[blockinfo]\nblast = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.blast\ngff1 = ${i}.gff\ngff2 = Bambusa_pervariabilis_Dendrocalamopsis_daii.gff\nlens1 = ${i}_length.txt\nlens2 = Bambusa_pervariabilis_Dendrocalamopsis_daii_length.txt\ncollinearity = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.icl\nscore = 100\nevalue = 1e-5\nrepeat_number = 10\nposition = order\nks = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.ks\nks_col = ks_NG86\nsavefile = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii_block.csv\n\n[correspondence]\nblockinfo =  ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii_block.csv\nlens1 = ${i}_length.txt\nlens2 = Bambusa_pervariabilis_Dendrocalamopsis_daii_length.txt\ntandem = true\ntandem_length = 200\npvalue = 0.2\nblock_length = 5\ntandem_ratio = 0.5\nmultiple  = 1\nhomo = -1,1\nsavefile = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii_Correspondence.csv\n\n[kspeaks]\nblockinfo = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii_Correspondence.csv\npvalue = 0.2\ntandem = true\nblock_length = 5\nks_area = 0,10\nmultiple = 1\nhomo = -1,1\nfontsize = 9\narea = 0,3\nfigsize = 10,6.18\nsavefig = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii_Kspeaks.png\nsavefile = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii_Kspeaks.csv\n\n[peaksfit]\nblockinfo = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii_Kspeaks.csv\nmode = median\nbins_number = 200\nks_area = 0,10\nfontsize = 9\narea = 0,3\nfigsize = 10,6.18\nshadow = true\nsavefig = ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii_Peaksfit.png\n\" > ${i}_Bambusa_pervariabilis_Dendrocalamopsis_daii.conf\ndone<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5ca73e4 elementor-widget elementor-widget-code-highlight\" data-id=\"5ca73e4\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"code-highlight.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"prismjs-okaidia copy-to-clipboard \">\n\t\t\t<pre data-line=\"\" class=\"highlight-height language-bash line-numbers\">\n\t\t\t\t<code readonly=\"true\" class=\"language-bash\">\n\t\t\t\t\t<xmp>for i in Dendrocalamus_latiflorus_Bambusa_pervariabilis_Dendrocalamopsis_daii.conf Guadua_angustifolia_Bambusa_pervariabilis_Dendrocalamopsis_daii.conf Melocanna_humilis_Bambusa_pervariabilis_Dendrocalamopsis_daii.conf Olyra_latifolia_Bambusa_pervariabilis_Dendrocalamopsis_daii.conf Oryza_sativa_Bambusa_pervariabilis_Dendrocalamopsis_daii.conf Phyllostachys_edulis_Bambusa_pervariabilis_Dendrocalamopsis_daii.conf\r\ndo\r\nwgdi -icl $i\r\nwgdi -ks $i\r\nwgdi -bi $i\r\nwgdi -c $i\r\nwgdi -kp $i\r\nwgdi -pf $i\r\ndone<\/xmp>\n\t\t\t\t<\/code>\n\t\t\t<\/pre>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>WGDI: \u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08WGD\uff09 1.\u6570\u636e\u51c6\u5907\u548c\u9884\u5904\u7406 WGDI\u8981\u6c42\uff081\uff09\u57fa\u56e0\u7ec4\u6587\u4ef6\uff1b\uff082\uff09\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6\uff08 &#8230; <a title=\"\u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08WGD\uff09\" class=\"read-more\" href=\"http:\/\/www.majunpeng.com\/index.php\/2024\/12\/09\/%e5%85%a8%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%8a%a0%e5%80%8d%ef%bc%88wgd%ef%bc%89\/\" aria-label=\"\u9605\u8bfb \u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08WGD\uff09\">\u9605\u8bfb\u66f4\u591a<\/a><\/p>\n","protected":false},"author":1,"featured_media":1367,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_crdt_document":"","footnotes":""},"categories":[6],"tags":[],"class_list":["post-1365","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-6"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v23.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>\u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08WGD\uff09 - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"http:\/\/www.majunpeng.com\/index.php\/2024\/12\/09\/\u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08wgd\uff09\/\" \/>\n<meta property=\"og:locale\" content=\"zh_CN\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08WGD\uff09 - \u5c0f\u9a6c\u751f\u4fe1\u65e5\u8bb0\" \/>\n<meta property=\"og:description\" content=\"WGDI: \u5168\u57fa\u56e0\u7ec4\u52a0\u500d\uff08WGD\uff09 1.\u6570\u636e\u51c6\u5907\u548c\u9884\u5904\u7406 WGDI\u8981\u6c42\uff081\uff09\u57fa\u56e0\u7ec4\u6587\u4ef6\uff1b\uff082\uff09\u57fa\u56e0\u7ec4\u6ce8\u91ca\u6587\u4ef6\uff08 ... \u9605\u8bfb\u66f4\u591a\" \/>\n<meta property=\"og:url\" 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