半成品推理仿真工具。为了描述侧化的特征，将特征映射到物种树上
heist-hemiplas的Python项目详细描述
抢劫
HemiplasyI参考S模拟Tool
作者：
马特·吉布森（gibsomat@indiana.edu）
马克·希宾斯（mhibbins@indiana.edu）
依赖项：
安装
git clone https://github.com/mhibbins/heist
cd heist
python setup.py install
使用
^{pr2}$输入文件
输入文件是修改的NEXUS格式。一个最小的例子包括一棵树（newick格式）和至少两个用set derived命令保存的分类单元集。如果用set outgroup指定了一个outgroup，则树将被修剪为只包含与模拟相关的分类单元（即，包含派生分类单元的子类）+outgroup。在
#NEXUS
begin trees;
tree tree_1 = (spA:0.002,(spB:0.001,((spC:0.0004,spD:0.0008)10.0:0.0005,(spE:0.0006,spF:0.0004)8.0:0.0004)15:0.0009)90.0:0.005);
end;
begin hemiplasytool;
set derived taxon=spB
set derived taxon=spD
set derived taxon=spF
end;
树种树
纽克格式的树种树。分支长度必须为每个站点的平均替换量，并且分支必须用一致性因子标记。IQTree可用于执行此操作。在
If your tree is already ultrametric and in coalescent units, you can supply this directly if you add the flag
set type coalto the input file.
特征
使用
set derived taxon="species in tree"
渗入
导入事件可以用
set introgression source="species in tree" dest="species in tree" prob=[float_value] timing=[float_value]
注意，必须以聚结单位指定时间。因此，我们建议首先通过^{
示例：
python -m hemiplasytool -n 100000 -x 5 -p ~/msdir/ms -g ~/Seq-Gen-1.3.4/seq-gen -o test_w_introgression -v test/input_test_small_intro_v2.txt
输出：
将生成三个输出文件。主要输出test_w_introgression.txt，一个基因树文件test_w_introgression.trees，包含所有观察到的拓扑结构，以及突变分布图test_w_introgression.dist.png。在
### INPUT SUMMARY ###
Integer Code Taxon Name
1: sp1
2: sp2
3: sp3
4: sp4
5: sp5
6: sp6
The species tree (smoothed, in coalescent units) is:
(1:2.78984,(2:2.09238,((3:0.69746,4:0.69746)1:0.69746,(5:0.69746,6:0.69746)1:0.69746)1:0.69746)1:0.69746);
_________________________________ 1
|
_| _________________________ 2*
| |
|_______| ________ 3
| _______|
| | |________ 4*
|________|
| ________ 5
|_______|
|________ 6*
3 taxa have the derived state: 2, 4, 6
With homoplasy only, 3 mutations are required to explain this trait pattern (Fitch parsimony)
Introgression from taxon 4 into taxon 6 occurs at time 0.3 with probability 0.05
5.00e+05 simulations performed
### RESULTS ###
70 loci matched the species character states
"True" hemiplasy (1 mutation) occurs 14 time(s)
Combinations of hemiplasy and homoplasy (1 < # mutations < 3) occur 30 time(s)
"True" homoplasy (>= 3 mutations) occurs 26 time(s)
70 loci have a discordant gene tree
0 loci are concordant with the species tree
4 loci originate from an introgressed history
66 loci originate from the species history
Distribution of mutation counts:
# Mutations # Trees
On all trees:
1 14
2 30
3 25
4 1
On concordant trees:
# Mutations # Trees
On discordant trees:
# Mutations # Trees
1 14
2 30
3 25
4 1
Origins of mutations leading to observed character states for hemiplasy + homoplasy cases:
Tip mutation Internal branch mutation Tip reversal
Taxa 2 3 27 0
Taxa 4 3 27 0
Taxa 6 0 30 0
### OBSERVED GENE TREES ###
_________________ 4
______________|
| | ________________ 3
| ||
| | _______ 5
_| |________|
| |_______ 6*
|
| _____________________________ 1
|___|
|_____________________________ 2
This topology occured 1 time(s)
____________ 3
____________________|
| |____________ 5
_|
| ________________________ 1
|________|
| __________________ 2
|____|
| __________ 4
|_______|
|__________ 6*
This topology occured 4 time(s)
_________________________ 2
______|
| | __________________ 5
| |______|
| | _______________ 4
_| |__|
| |_______________ 6*
|
| _______________________________ 1
|_|
|_______________________________ 3
...
有关完整输出，请参见test_w_introgression.txt.txt。在
子模块
一旦安装，两个附加程序将在命令行可用：newick2ms和{
新ick2ms
usage: newick2ms [-h] input
Tool for converting a newick string to ms-style splits. Note that this only
makes sense if the input tree is in coalescent units.
positional arguments:
input Input newick string file
optional arguments:
-h, --help show this help message and exit
亚粘土
usage: subs2coal [-h] input
Tool for converting a newick string with branch lengths in subs/site to a
neewick string with branch lengths in coalescent units. Input requires gene or
site-concordancee factors as branch labels
positional arguments:
input Input newick string file
optional arguments:
-h, --help show this help message and exit
海斯麦奇
usage: heistmerge [-h] [-d] [inputs [inputs ...]]
Merge output files from multiple HeiST runs. Useful for simulating large trees
by running multiple batch jobs.
positional arguments:
inputs Prefixes of output files to merge or a directory (supply -d flag
as well)
optional arguments:
-h, --help show this help message and exit
-d Merge all files in a directory
heistMerge将把合并的输出摘要写入标准输出，并创建一个新文件merged_trees.trees，其中包含所有观察到的焦点基因树。在
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