使用 phylip构建进化树
001、测试数据转换为vcf格式
[root@PC1 test]# ls test.map test.ped [root@PC1 test]# plink --file test --recode vcf-iid --out test
002、将vcf转为phylip格式文件
[root@PC1 test]# /opt/TASSEL5/run_pipeline.pl -importGuess test.vcf -ExportPlugin -saveAs test.phy -format Phylip_Inter [root@PC1 test]# ls test.map test.ped test.phy test.vcf
003、生成dandist的配置文件
[root@PC1 test]# echo -e "test.phy\nY" > dnadist.cfg [root@PC1 test]# ls dnadist.cfg test.map test.ped test.phy test.vcf
004、运行dnadist程序，生成距离矩阵文件
[root@PC1 test]# /home/software/phylip/phylip-3.697/exe/dnadist < dnadist.cfg >dnadist.log [root@PC1 test]# ls dnadist.cfg dnadist.log outfile test.map test.ped test.phy test.vcf
005、生成neighbor程序需要的配置文件
[root@PC1 test]# mv outfile infile.dist [root@PC1 test]# ls dnadist.cfg dnadist.log infile.dist test.map test.ped test.phy test.vcf [root@PC1 test]# echo -e "infile.dist\nY" > neighbor.cfg [root@PC1 test]# ls dnadist.cfg dnadist.log infile.dist neighbor.cfg test.map test.ped test.phy test.vcf
006、构建nj树
[root@PC1 test]# /home/software/phylip/phylip-3.697/exe/neighbor < neighbor.cfg >nj.log [root@PC1 test]# ls dnadist.cfg dnadist.log infile.dist neighbor.cfg nj.log outfile outtree test.map test.ped test.phy test.vcf
007、整理结果格式
[root@PC1 test]# less infile.dist | tr '\n' '|'| sed 's/| / /g' | tr '|' '\n' >infile.dist.table [root@PC1 test]# ls dnadist.cfg dnadist.log infile.dist infile.dist.table neighbor.cfg nj.log outfile outtree test.map test.ped test.phy test.vcf [root@PC1 test]# less outtree | tr '\n' ' '|sed 's/ //g' > outtree.nwk [root@PC1 test]# ls dnadist.cfg dnadist.log infile.dist infile.dist.table neighbor.cfg nj.log outfile outtree outtree.nwk test.map test.ped test.phy test.vcf
008、利用 outtree.nwk 文件在itol网页中构树
01、进入itol官网：
02、点击upload a tree
03、上传文件
04、草图
参考：https://mp.weixin.qq.com/s?__biz=Mzg4NDc4MjkxNA==&mid=2247488928&idx=1&sn=ee10c8b8020b80696c2cc88f3eb1ad2a&chksm=cfb3b78df8c43e9bf2b420ecb654e0306b9da1947c4e390f74ca57ff2985c57c9b396a27b423&scene=178&cur_album_id=2485246989195051008#rd
