thirdkind

绘制允许1、2或3个协调级别的系统发育树

构建包含事件（丢失、复制、物种形成、转移）的系统发育协调（或不协调）树的SVG表示。

• 输入一个newick或phyloxml文件 -> 树的节点事件的SVG表示

• 输入一个recphyloxml文件 -> 关联物种（或宿主）'上层'树内的基因（或共生体）'下层'树的SVG表示

• 输入一组recphyloxml文件 -> 所有基因（或共生体）'下层'树在关联物种（或宿主）'上层'树中的SVG表示，或仅1个基因树，包含所有基因（或共生体）的转移，允许可视化不同场景或历史中的转移。

• 输入两个嵌套的recphyloxml文件 -> 几个SVG表示，可以显示3级协调（例如基因/共生体/宿主）

主页

主页： https://github.com/simonpenel/thirdkind/wiki

关键词

系统发育、协调树、系统发育树、协调、可视化、svg、recphyloxml、phyloxml、3级协调、基因转移、物种形成、复制、丢失

格式

phyloXML、recPhyloXML、有根的newick（NHX标签将不予考虑）。

图形界面

一个专门用于thirdkind图形界面的Web服务器可供在此处使用：http://thirdkind.univ-lyon1.fr/

2级可视化示例

单个基因与物种树协调

https://raw.githubusercontent.com/simonpenel/thirdkind/74b9c84a5b2ed84ff5230fc3a52af856b9aba53d/output_examples/thirdkind_example1.svg

相同的基因协调，但没有物种树

https://raw.githubusercontent.com/simonpenel/thirdkind/74b9c84a5b2ed84ff5230fc3a52af856b9aba53d/output_examples/thirdkind_example1_bis.svg

多个基因协调

https://raw.githubusercontent.com/simonpenel/thirdkind/70a7a11aa89eda61926c5cabf221f47bb44e3409/output_examples/thirdkind_example4.svg

使用recPhyloXML文件的实际长度

https://raw.githubusercontent.com/simonpenel/thirdkind/b084872f02a758702e0f90543c715862729166a5/output_examples/thirdkind_real_length.svg

使用“自由生活”的物种

https://raw.githubusercontent.com/simonpenel/thirdkind/0f8ff64838fc7676b2e98542e953c4ccc9f45c62/output_examples/thirdkind_fl_example2.svg

多个 "spTree"

https://raw.githubusercontent.com/simonpenel/thirdkind/79344589aa8b91a909386d22c95a01bc8c795396/output_examples/thirdkind_multspec.svg

多基因树与冗余转移的协调。仅显示1个基因树和红色转移，透明度根据转移的丰度而定

https://raw.githubusercontent.com/simonpenel/thirdkind/70a7a11aa89eda61926c5cabf221f47bb44e3409/output_examples/thirdkind_example2.svg

3级可视化输出示例

示例1

协调的共生树及其相关基因树：[链接](https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example3_mapped_1.svg)

共生体-宿主协调加上映射的基因转移：[链接](https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example3_mapped_2.svg)

宿主树及其相关基因树：[链接](https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example3_mapped_3.svg)

示例2

协调的共生树及其相关基因树：[链接](https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example4_mapped_1.svg)

共生体-宿主协调加上映射的基因转移：[链接](https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example4_mapped_2.svg)

宿主树及其相关基因树：[链接](https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example4_mapped_3.svg)

安装

thirdkind 使用 Rust 编写。代码使用 Cargo 管理，并在 crates.io 上发布。

安装 cargo

curl https://sh.rustup.rs -sSf | sh

或对于 Windows，请参阅 [安装指南](https://doc.rust-lang.net.cn/cargo/getting-started/installation.html)

注意

由于 Rust 尚未包含自己的链接器，构建 thirdkind 需要 C 编译器（如 gcc）作为链接器。如果不是这种情况，则需要安装 Rust 所需的基本构建工具。

sudo apt install build-essential

安装 Cargo 后，只需打开一个新终端并输入

cargo install thirdkind
thirdkind

您也可以从源代码安装。如果您想使用示例，请在此处克隆或下载源代码 [GitHub 仓库](https://github.com/simonpenel/thirdkind) 并输入

cargo build --release
target/release/thirdkind -h

运行二进制文件

读取 Newick、PhyloXML 或 recPhyloXML 文件并创建 SVG。

格式根据文件名猜测（默认为 Newick）

Usage: thirdkind [OPTIONS] --input-file <INPUT_FILE>

Options:
  -a, --output-transfer-analysis
          Display transfers analysis (with -m and -t options)
  -A, --starting-node <STARTING_NODE>
          Display transfers starting from this node only
  -b, --browser
          Open svg in browser    
  -B, --display-br-length
          With option -l, display branch length
  -c, --conf-file <CONF_FILE>
          Use configuration file
  -C, --gene-colors <GENE_COLORS>
          Define colors for gene trees. For example: "red,violet,#4A38C4,orange"
  -d, --gene-fontsize <GENE_FONTSIZE>
          Set font size for gene trees
  -D, --species-fontsize <SPECIES_FONTSIZE>
          Set font size for species trees
  -e, --free-living-sup
          "free living" option : nodes associated to FREE_LIVING are drawned in an external tree and superposed in case of multiple genes
  -E, --free-living-shi
          "free living" option : nodes associated to FREE_LIVING are drawned in an external tree and shifted in case of multiple genes
  -f, --input-file <INPUT_FILE>
          Input tree file (accepted format: newick, phyloXML, recPhyloXML)
  -F, --format <FORMAT>
          Force format phyloXML/recPhyloXML
  -g, --nested <NESTED>
          1st level input file (for example a gene-symbiote file with -f defining a 2nd level symbiote-host file)
  -G, --gene-phylo <GENE_PHYLO>
          Display the gene number <GENE_PHYLO> in phyloxml style (no species tree)
  -H, --height <HEIGHT>
          Height:  multiply the tree height by factor <HEIGHT>
  -i, --internal-gene-node
          Display internal gene node names
  -I, --internal-species-node        
          Display internal species node names
  -J, --display-transfers-abundance
          With option -t, display the abundance of redudant transfers
  -k, --symbol-size <SYMBOL_SIZE>    
          Size of the circles, crosses, squares, etc
  -K, --bezier <BEZIER>
          Bezier parameter: curvature of the transfers and branches leading to free living organisms
  -l, --branch-length <BRANCH_LENGTH>
          Use branch length, multiplied by the given factor
  -L, --landscape
          Display as landscape
  -m, --multiple
          The input file (-f) is a list of recphyloxml files
  -M, --midway
          Display duplication node at midway in the branch
  -n, --gene-tree-list <GENE_TREE_LIST>
          List of the indexes of the gene trees to be displayed. For example: 1,2,6,9. If 0, only the species ('upper') tree is displayed
  -N, --ending-node <ENDING_NODE>
          Display transfers ending to this node only
  -o, --output <OUTPUT>        
          Set the name of the output file or the prefix of the output files
  -O, --optimise
          Switching nodes in order to minimise transfer crossings (under development)
  -p, --uniform
          Species tree uniformisation. All the branches of species have the same width
  -q, --node-colors <NODE_COLORS>
          Nodes to be coloured : the descendants of each nodes will be drawn with a different colour. For example: "m3,m25,m36"
  -Q, --background <BACKGROUND>
          Background colour
  -r, --ratio <RATIO>
          Set the ratio between width of species and gene tree. Default is 1.0, you usualy do not need to change it
  -s, --species-only
          Display species tree only in phyloxml style
  -S, --node-support
          Display node support
  -t, --threshold <THRESHOLD>    
          Redudant transfers are displayed as one, with opacity according to abundance and only if abundance is higher than <THRESHOLD>. Only one gene is displayed    
  -T, --threshold-select <THRESHOLD_SELECT>
          With option -t, select the index of the gene to display. If set to 0, no gene is displayed
  -u, --threshold-nested <THRESHOLD_NESTED>
          With -g, same as -t, but apply to the '-f' input file, and -t will apply to the '-g' file
  -U, --threshold-nested-select <THRESHOLD_NESTED_SELECT>
          Same as -T with -t, but for -u
  -v, --verbose
          Verbose mode
  -W, --width <WIDTH>
          Width:  multiply the tree height by factor <WIDTH>
  -x, --tidy
          Tidy mode (non-layered tidy tree layout)
  -X, --tidy-clean
          Tidy mode, avoiding leave names superposition
  -z, --gene-thickness <GENE_THICKNESS>
          Thickness of the gene tree
  -Z, --species-thickness <SPECIES_THICKNESS>
          Thickness of the species tree
  -h, --help
          Print help
  -V, --version
          Print version

Note on -b option : you must set a browser as default application for opening  svg file

Note on -g option : this will generate 3-levels reconciliation svg files.

For example you may input a gene-symbiote recphyloxml file  with -g and symbiote-host recphyloxml file with -f
The -t/-u options are not totally implemented for the 3-levels reconciliation svg output files.

Note on -x/-X options : the non-layered tidy tree layout is described in :
	'van der Ploeg, A. 2014. Drawing non-layered tidy trees in linear time. 
	Software: Practice and Experience, 44(12): 1467–1484.'

Input format is guessed according to the file name extension:
 	.phyloxml    => phyloXML
    .xml         => recPhyloxml
    .recphyloxml => recPhyloXML
    .recPhyloXML => recPhyloXML
    .recphylo    => recPhyloXML
    any other    => newick

示例

thirdkind -f recphylo_examples/FAM000297_reconciliated.recphylo  -b
thirdkind -f recphylo_examples/concat.xml -b -t 0
thirdkind -f recphylo_examples/hote_parasite_page4_BL.recphylo  -b -l 1
thirdkind -f recphylo_examples/testfiles -m -b -t 3 -J
thirdkind -f recphylo_examples/test2/hote_parasite_page2.recphylo  -g recphylo_examples/test2/gene_parasite_page2.recphylo  -b  
thirdkind -f recphylo_examples/test1_mult_parasite/rechp_dtl.recphyloxml -g recphylo_examples/test1_mult_parasite/recgs_mult_host_dtl.recphyloxml -b
thirdkind -f newick_examples/virus.nhx -l 4  -b
thirdkind -f newick_examples/virus.nhx -l 4 -x  -b
thirdkind -f newick_examples/virus.nhx -l 4 -X  -b

配置文件

您可以使用 -c 选项配置 SVG 的某些功能。

默认值是 "config_default.txt" 文件中的值。

修改默认值并将其保存到 "my_config.txt" 中，然后输入

thirdkind -f recphylo_examples/FAM000600_reconciliated_big.recphylo -c my_config.txt -b

配置文件内容

species_color:pink
species_opacity:0.9
single_gene_color:blue
gene_opacity:0.9
species_police_color:orange
species_police_size:12
gene_police_size:10
bezier:1

使用 API light_phylogeny

thirdkind 使用 light_phylogeny 库

https://github.com/simonpenel/light_phylogeny/wiki

recPhyloXML 文档

请参阅 [recPhyloXML 网站](http://phylariane.univ-lyon1.fr/recphyloxml/)

recPhyloXML 论文：[链接](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198865/)

phyloXML 文档

请参阅：[phyloXML 网站](http://www.phyloxml.org/)

phyloXML 论文：[链接](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774328/)

引用

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac062/6525213

联系

https://lbbe.univ-lyon1.fr/fr/annuaire-des-membres/penel-simon

许可

CECILL：[链接](https://choosealicense.com/licenses/cecill-2.1/)