Hennig86：修订间差异
Malacology（留言 | 贡献） init |
Malacology（留言 | 贡献） 小 →简介 |
||
| （未显示同一用户的7个中间版本） | |||
| 第1行： | 第1行： | ||
= | = 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的系统发育软件。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。 | |||
Hennig86 于 1988 由 James S. Farris 编写并发布，是第一个能在 MS-DOS IBM-PC | |||
注意！Hennig86 不是 TNT 的前身！ | 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。 | 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> | <span id="基础-log"></span> | ||
== 基础 log == | |||
<code>display*</code> 让也在终端显示。 | <code>display*</code> 让也在终端显示。 | ||
| 第45行： | 第43行： | ||
display*;</pre> | display*;</pre> | ||
<span id="基础-help"></span> | <span id="基础-help"></span> | ||
== 基础 help == | |||
<pre>quote This function help send comments to log file; | <pre>quote This function help send comments to log file; | ||
quote Here are functions; | quote Here are functions; | ||
assist;</pre> | assist;</pre> | ||
== 打开文件 == | |||
<code>view</code> 查看文件。 | <code>view</code> 查看文件。 | ||
| 第57行： | 第56行： | ||
view CZ.SS; | view CZ.SS; | ||
procedure CZ.SS;</pre> | 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 | <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 | ||
| 第65行： | 第65行： | ||
outgroup;</pre> | outgroup;</pre> | ||
<span id="查看-character-weighting"></span> | <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。 | <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。 | ||
| 第80行： | 第80行： | ||
cget 1; | cget 1; | ||
ccode;</pre> | 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。 | <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。 | ||
| 第91行： | 第91行： | ||
tplot; | tplot; | ||
tlist; | tlist; | ||
quote Store it into internal tree file | quote Store it into internal tree file 1; | ||
keep 1;</pre> | keep 1;</pre> | ||
== 查看树的信息 == | |||
<code>xsteps</code>主要用于查看树的信息。 | <code>xsteps</code>主要用于查看树的信息。 | ||
| 第103行： | 第103行： | ||
quote Display max/min steps for per character; | quote Display max/min steps for per character; | ||
steps;</pre> | 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。 | <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。 | ||
| 第114行： | 第114行： | ||
mhennig*; | mhennig*; | ||
bb*; | bb*; | ||
quote Store them into internal tree file | quote Store them into internal tree file 2; | ||
keep 2;</pre> | keep 2;</pre> | ||
== 基础合意树 == | |||
合意树保存到内部树文件 3。 | 合意树保存到内部树文件 3。 | ||
| 第125行： | 第125行： | ||
keep 3;</pre> | keep 3;</pre> | ||
<span id="successive-weighting"></span> | <span id="successive-weighting"></span> | ||
== successive weighting == | |||
<code>ccode</code>weighting 搜索保存到内部树文件 4。 | <code>ccode</code>weighting 搜索保存到内部树文件 4。 | ||
| 第142行： | 第142行： | ||
quote Store it into internal tree file 5; | quote Store it into internal tree file 5; | ||
keep 5;</pre> | keep 5;</pre> | ||
== 穷举法 == | |||
<code>ie*;</code> 使用穷举法，保存到内部树文件 6。 | <code>ie*;</code> 使用穷举法，保存到内部树文件 6。 | ||
| 第156行： | 第156行： | ||
quote Store it into internal tree file 7; | quote Store it into internal tree file 7; | ||
keep 7;</pre> | keep 7;</pre> | ||
== 时间测试 == | |||
<code>watch-;</code> 停止测试时间 | <code>watch-;</code> 停止测试时间 | ||
| 第162行： | 第163行： | ||
<pre>quote Stop watch time; | <pre>quote Stop watch time; | ||
watch-;</pre> | 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。 | <code>get</code> 切换不同的内部树文件， <code>tlist</code> 查看文件。 | ||
| 第172行： | 第173行： | ||
get 5; | get 5; | ||
tlist; | tlist; | ||
tsave | tsave contre;</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。 | <code>erase</code> 删除内部树文件， <code>files</code> 查看内部树文件有哪些。 | ||
| 第180行： | 第181行： | ||
erase 1; | erase 1; | ||
files;</pre> | files;</pre> | ||
== 退出 == | |||
<code>log/;</code> 停止记录，<code>yama</code> 退出 Hennig86。 | <code>log/;</code> 停止记录，<code>yama</code> 退出 Hennig86。 | ||
| 第187行： | 第188行： | ||
log/; | log/; | ||
yama;</pre> | yama;</pre> | ||
== 查看编辑树 == | |||
<code>xx</code> 查看树。 | <code>xx</code> 查看树。 | ||
| 第195行： | 第196行： | ||
/ | / | ||
;</pre> | ;</pre> | ||
= 所有命令一览 = | |||
<pre> | |||
Dox -- Online Help File for Hennig86, Version 1.5 | |||
Copyright (c) James S. Farris | |||
All rights reserved. | |||
assist batch bb bytes ccode cget ckeep | |||
display erase files get hennig ie keep | |||
log mhennig nelsen outgroup procedure quote reroot | |||
steps tchoose tlist tplot tread tsave txascii | |||
view watch xread xsteps xx yama | |||
assist list available commands | |||
batch turn on batch switch | |||
batch - turn it off | |||
bb produce multiple trees by branch breaking | |||
bb * use all available tree space | |||
bytes display bytes of free ram | |||
ccode control character coding | |||
/ set weight [ activate ] deactivate + additive - nonadditive | |||
ccode ; display codings | |||
cget x set coding from code file x | |||
ckeep x save current coding in code file x | |||
display short listings to display | |||
display - no listing to display | |||
display * all listing to display | |||
erase s delete tree files in scope s | |||
files display directory of treefiles | |||
get x make tree file x current | |||
hennig calculate single tree | |||
hennig * use branch breaking | |||
ie find trees by implicit enumeration | |||
ie - find just one tree | |||
ie * use all available tree space | |||
keep x save current tree file as tree file x | |||
log n open dos file n as new log file | |||
log - deactivate log file | |||
log * activate it | |||
log / close it | |||
mhennig calculate multiple trees | |||
mhennig * use branch breaking | |||
nelsen calculate nelson consensus tree | |||
outgroup control outgroup | |||
[ ingroup ] outgroup | |||
outgroup = set outgroup to list | |||
outgroup ; list outgroup alphabetically | |||
procedure n open dos file n as procedure file | |||
procedure - deactivate procedure file | |||
procedure * activate it | |||
procedure / close it | |||
quote copy message | |||
reroot current treefile according to current outgroup | |||
steps display max/min steps per character | |||
tchoose s select trees in scope s from current tree file | |||
tlist display trees in parenthetical notation | |||
tplot produce tree diagrams | |||
tread read trees | |||
tsave n save current tree file on dos file n | |||
txascii use extended ascii characters in tree plots | |||
txascii - don't | |||
view n inspect dos file n | |||
view * close and inspect current log file | |||
watch turn on stopwatch | |||
watch - turn it off | |||
xread read character data | |||
xsteps diagnose trees in current tree file | |||
xsteps h list possible states for hypothetical ancestors | |||
xsteps c list character fits | |||
xsteps m list best/worst fits | |||
xsteps l list tree lengths | |||
xsteps u produce file of distinct trees | |||
xsteps w set character weights according to fits | |||
xx display and modify diagnosed tree | |||
yama return to dos | |||
</pre> | |||
[[分类:Bioinformatics]] | |||
2023年7月26日 (三) 09:04的最新版本
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的系统发育软件。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
Hennig86 自带示例文件如下，跟 TNT 完全兼容。
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 / ;
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 1; 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 2; 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
ccodeweighting 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 contre;
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 \ / ;
所有命令一览
Dox -- Online Help File for Hennig86, Version 1.5
Copyright (c) James S. Farris
All rights reserved.
assist batch bb bytes ccode cget ckeep
display erase files get hennig ie keep
log mhennig nelsen outgroup procedure quote reroot
steps tchoose tlist tplot tread tsave txascii
view watch xread xsteps xx yama
assist list available commands
batch turn on batch switch
batch - turn it off
bb produce multiple trees by branch breaking
bb * use all available tree space
bytes display bytes of free ram
ccode control character coding
/ set weight [ activate ] deactivate + additive - nonadditive
ccode ; display codings
cget x set coding from code file x
ckeep x save current coding in code file x
display short listings to display
display - no listing to display
display * all listing to display
erase s delete tree files in scope s
files display directory of treefiles
get x make tree file x current
hennig calculate single tree
hennig * use branch breaking
ie find trees by implicit enumeration
ie - find just one tree
ie * use all available tree space
keep x save current tree file as tree file x
log n open dos file n as new log file
log - deactivate log file
log * activate it
log / close it
mhennig calculate multiple trees
mhennig * use branch breaking
nelsen calculate nelson consensus tree
outgroup control outgroup
[ ingroup ] outgroup
outgroup = set outgroup to list
outgroup ; list outgroup alphabetically
procedure n open dos file n as procedure file
procedure - deactivate procedure file
procedure * activate it
procedure / close it
quote copy message
reroot current treefile according to current outgroup
steps display max/min steps per character
tchoose s select trees in scope s from current tree file
tlist display trees in parenthetical notation
tplot produce tree diagrams
tread read trees
tsave n save current tree file on dos file n
txascii use extended ascii characters in tree plots
txascii - don't
view n inspect dos file n
view * close and inspect current log file
watch turn on stopwatch
watch - turn it off
xread read character data
xsteps diagnose trees in current tree file
xsteps h list possible states for hypothetical ancestors
xsteps c list character fits
xsteps m list best/worst fits
xsteps l list tree lengths
xsteps u produce file of distinct trees
xsteps w set character weights according to fits
xx display and modify diagnosed tree
yama return to dos