Hennig86:修订间差异
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[[分类:Bioinformatics]] |
2023年7月20日 (四) 19:04的版本
Hennig86
简介
Hennig86 于 1988 由 James S. Farris 编写并发布,是第一个能在 MS-DOS IBM-PC 及其兼容性机器上运行良好的简约法软件。最初售价 50 美元,目前已经不再分发并且已经被 TNT 取代,但是他的文件风格以及部分命令已经被众多软件吸取。
注意!Hennig86 不是 TNT 的前身!
分析基础
你需要安装 DOSBox 软件,并且具备很少的 DOS 命令基础,比如 MOUNT
TYPE
等。
文件基础
示例文件如下,跟 TNT 完全兼容。
xread 'Data saved from TNT' 10 15 OUTGROUP 1011110011 TAX1 0101100000 TAX2 1011000111 TAX3 1000111010 TAX4 1111010010 TAX5 1010010001 TAX6 1101010111 TAX7 0101010010 TAX8 1000001101 TAX9 0000100001 TAX10 1000111010 TAX11 0010011101 TAX12 0111111111 TAX13 1011010110 TAX14 0101110001 ; proc/;
分析流程
基础 log
display*
让也在终端显示。
log hennig.log; display*;
基础 help
quote This function help send comments to log file; quote Here are functions; assist;
打开文件
view
查看文件。
quote Open data file and view it; view CZ.SS; procedure CZ.SS;
设置外群
/num
设置多个外群中相对外的 prime outgroup
。0.2
中的 .
代表范围
quote Set outgroups and prime outgroup (0-2 are outgroups and 0 is prime outgroup); outgroup = 0.2 /0; outgroup;
查看 character weighting
ckeep
和 cget
用于快速保存、选择某一套 character weighting 以及 additive (ccode+.;
) 和 non-additive (ccode-.;
)。 ccode;
查看状态。
quote Check character weighting realted settings and store them in internal file 1; ccode-.; ckeep 1; ccode; quote Set them as additive character and save as internal file 2; ccode+.; ccode; ckeep 2; quote Check eveything as additive, now run cget to obtain previous config; cget 1; ccode;
基础搜索树
hennig
bb
都是对单个树计算, keep
对树进行划归组保存为内部树文件。
quote Start an example on how to search tree; hennig; bb; quote Here to disable ascii and have a look; txascii-; tplot; tlist; quote Store it into internal tree file 0; keep 1;
查看树的信息
xsteps
主要用于查看树的信息。
quote Output Tree Length based on tree number, same with xsteps; xsteps l; quote Output characters' steps RI CI; xsteps c; quote Display max/min steps for per character; steps;
进阶搜索树
hennig
bb
的 m
前缀是多个树的意思,*
后缀是指树的数量要不要做限制。这个搜索保存到内部树文件 2。watch
查看每个命令耗费的时间。
quote Check current memory; bytes; quote Start watch time; watch; quote Start search heavily and swap trees; mhennig*; bb*; quote Store them into internal tree file 1; keep 2;
基础合意树
合意树保存到内部树文件 3。
quote Generate strict consensus tree, all trees will be removed from memory; nelsen; quote Store it into internal tree file 3; keep 3;
successive weighting
ccode
weighting 搜索保存到内部树文件 4。
quote Successive Weighting can be enabled; xsteps w; ccode; mhennig*; bb*; quote Store them into internal tree file 4; keep 4;
合意树保存到内部树文件 5。
quote Generate strict consensus tree, all trees will be removed from memory; nelsen; quote Store it into internal tree file 5; keep 5;
穷举法
ie*;
使用穷举法,保存到内部树文件 6。
quote Search all the trees; ie*; quote Store them into internal tree file 6; keep 6;
合意树保存到内部树文件 7。
quote Generate strict consensus tree, all trees will be removed from memory; nelsen; quote Store it into internal tree file 7; keep 7;
时间测试
watch-;
停止测试时间
quote Stop watch time; watch-;
查看树
get
切换不同的内部树文件, tlist
查看文件。
quote Test internal tree files via get; files; get 3; tlist; get 5; tlist; tsave con.tre;
编辑内部树文件
erase
删除内部树文件, files
查看内部树文件有哪些。
quote Delete internal tree file; erase 1; files;
退出
log/;
停止记录,yama
退出 Hennig86。
quote Stop log and quit; log/; yama;
查看编辑树
xx
查看树。
xx \ / ;