查看“︁Hennig86”︁的源代码

= 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 <code>MOUNT</code> <code>TYPE</code> 等。

== 文件基础 ==

Hennig86 自带示例文件如下，跟 TNT 完全兼容。

<pre>
xread
'SALA -- BOLICK ADV. CLAD. 1:115-125 SALMEA (COMPOSITAE: HELIANTHEAE)'
24 11 
ANCT 
000000000000000000000000
SCAN 
000000100001210000000000
ORTH 
000000100001101000000000
OLIG 
100000100002010111000000
PALM 
000000100002000110100000
PETR 
001100100000000000011000
CALE 
100021011110000000000000
GLAB 
000200111100000000000001
MONT 
321010111100000000000000
INSI 
220000011110000000000110
PAUC 
210010011110000000000101

 ;
proc /  ;
</pre>

== 分析流程 ==

<span id="基础-log"></span>
=== 基础 log ===

<code>display*</code> 让也在终端显示。

<pre>log hennig.log;
display*;</pre>
<span id="基础-help"></span>
=== 基础 help ===

<pre>quote This function help send comments to log file;
quote Here are functions;
assist;</pre>
=== 打开文件 ===

<code>view</code> 查看文件。

<pre>quote Open data file and view it;
view CZ.SS;
procedure CZ.SS;</pre>
=== 设置外群 ===

<code>/num</code> 设置多个外群中相对外的 <code>prime outgroup</code>。<code>0.2</code> 中的 <code>.</code> 代表范围

<pre>quote Set outgroups and prime outgroup (0-2 are outgroups and 0 is prime outgroup);
outgroup = 0.2 /0;
outgroup;</pre>
<span id="查看-character-weighting"></span>
=== 查看 character weighting ===

<code>ckeep</code> 和 <code>cget</code> 用于快速保存、选择某一套 character weighting 以及 additive (<code>ccode+.;</code>) 和 non-additive (<code>ccode-.;</code>)。 <code>ccode;</code> 查看状态。

<pre>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;</pre>
=== 基础搜索树 ===

<code>hennig</code> <code>bb</code> 都是对单个树计算， <code>keep</code> 对树进行划归组保存为内部树文件。

<pre>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;</pre>
=== 查看树的信息 ===

<code>xsteps</code>主要用于查看树的信息。

<pre>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;</pre>
=== 进阶搜索树 ===

<code>hennig</code> <code>bb</code> 的 <code>m</code> 前缀是多个树的意思，<code>*</code> 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。<code>watch</code> 查看每个命令耗费的时间。

<pre>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;</pre>
=== 基础合意树 ===

合意树保存到内部树文件 3。

<pre>quote Generate strict consensus tree, all trees will be removed from memory;
nelsen;
quote Store it into internal tree file 3;
keep 3;</pre>
<span id="successive-weighting"></span>
=== successive weighting ===

<code>ccode</code>weighting 搜索保存到内部树文件 4。

<pre>quote Successive Weighting can be enabled;
xsteps w;
ccode;
mhennig*;
bb*;
quote Store them into internal tree file 4;
keep 4;</pre>
合意树保存到内部树文件 5。

<pre>quote Generate strict consensus tree, all trees will be removed from memory;
nelsen;
quote Store it into internal tree file 5;
keep 5;</pre>
=== 穷举法 ===

<code>ie*;</code> 使用穷举法，保存到内部树文件 6。

<pre>quote Search all the trees;
ie*;
quote Store them into internal tree file 6;
keep 6;</pre>
合意树保存到内部树文件 7。

<pre>quote Generate strict consensus tree, all trees will be removed from memory;
nelsen;
quote Store it into internal tree file 7;
keep 7;</pre>
=== 时间测试 ===

<code>watch-;</code> 停止测试时间

<pre>quote Stop watch time;
watch-;</pre>
=== 查看树 ===

<code>get</code> 切换不同的内部树文件， <code>tlist</code> 查看文件。

<pre>quote Test internal tree files via get;
files;
get 3;
tlist;
get 5;
tlist;
tsave con.tre;</pre>
=== 编辑内部树文件 ===

<code>erase</code> 删除内部树文件， <code>files</code> 查看内部树文件有哪些。

<pre>quote Delete internal tree file;
erase 1;
files;</pre>
=== 退出 ===

<code>log/;</code> 停止记录，<code>yama</code> 退出 Hennig86。

<pre>quote Stop log and quit;
log/;
yama;</pre>
=== 查看编辑树 ===

<code>xx</code> 查看树。

<pre>xx
\
/
;</pre>
[[分类:Bioinformatics]]