We defined the ILS/IH index to represent the degree of Incomplete lineage sorting (ILS) and introgression (IH) among lineages. This tool can quickly detect and visualize ILS/IH index between lineages of tree results run by ASTRAL option -u 2 or -t -2, with short running time, helping users to preliminatively determine ILS and IH and screen lineages for further analysis.For more details of ILS/IH index, please see https://www.biorxiv.org/content/10.1101/2024.09.02.610893v1. Any nodes of phylogenetic tree can be regarded as consisting of two sister groups and one outgroup, and these three lineages can form three topologies q1, q2, q3 (as shown in the figure below),The topology with the highest proportion is denoted as q1. ILS/IH index is calculated based on the number and proportion of these topologies.
Figure. The three topological structures of gene trees Any combination of three lineages produces three topologies, When the ILS index is at its maximum of 100% and there is no IH, we expect q1 = q2 = q3 = 100%/3. When the IH index reaches 50% and there is no ILS, q1 = q2 = 50% is expected.

Executable version for Windows and Linux can be downloaded at https://figshare.com/articles/dataset/phytop_executable_versions_in_windows_and_linux/27276699

# run help for the executable version for Windows
phytop.exe -h
# run help for the executable version for Linux
phytop_linux -h

Download and install Phytop in Linux:

git clone https://github.com/zhangrengang/phytop
cd phytop

# install
conda env create -f phytop.yaml
conda activate phytop
python setup.py install

Start for example data:

cd example_data

Get barcharts:

phytop astral.tree

When runing ASTRAL, please use -u 2 (for C++ version, including astral, astral-pro and astral-hybrid etc.) or -t 2 (for JAVA version, including ASTRAL-III and ASTRAL-MP) option. Then, the output species tree from ASTRAL can be used as input to phytop.

├── /tmp          # Transition File (unused)
├── *.pdf         # Visualization of the tree file generated by astral
├── *.info.tsv    # The specific value of each node

The block diagram in PDF shows the ratio of q1, q2 and q3 of nodes. q2 and q3 are topologies that conflict with q1. Higher ILS-i or IH-i represent stronger ILS or IH respectively. In this example, there are strong ILS and IH among Juglans nigra, Juglans mandshurica, and (Juglans regia, Juglans sigillata). Since q2 is much larger than q3, we can roughly infer that there is strong IH from Juglans nigra and Juglans mandshurica to (Juglans regia, Juglans sigillata). There are almost no ILS and IH among Juglans regia, Juglans sigillata and outgroup, and this node can be considered as a well-resolved node. The below is an output figures of Phytop with default parameters: Figure. Visual result of Phytop on example data with default parameters. n represents the number of gene trees, P is the p-value of χ2 test to check whether the number of topologies q2 and q3 are equal, ILS-i and IH-i represent the calculated ILS index and IH index respectively, and ILS-e and IH-e represent the proportion of gene tree topological incongruence that can be explained by the ILS and IH, respectively.

usage: phytop [-h] [-alter NEWICK] [-g NEWICK] [-align] [-cp] [-branch_size BRANCH_SIZE] [-leaf_size LEAF_SIZE] [-sort]
              [-notext] [-figsize FIGSIZE] [-fontsize FONTSIZE] [-figfmt FIGFMT] [-polytomy_test] [-pie] [-pie_size PIE_SIZE]
              [-pie_fold PIE_FOLD] [-bl] [-test [TAXON/FILE [TAXON/FILE ...]]] [-astral_bin STR] [-outgroup STR]
              [-clades FILE] [-collapse [TAXON/FILE [TAXON/FILE ...]]] [-onshow TAXON/FILE [TAXON/FILE ...]]
              [-noshow TAXON/FILE [TAXON/FILE ...]] [-subset TAXON/FILE [TAXON/FILE ...]] [-pre STR] [-tmp DIR]
              NEWICK

Visualizing ILS/IH signals on species tree from ASTRAL.

optional arguments:
  -h, --help            show this help message and exit

Input:

  NEWICK                Species tree output by ASTRAL (using option `-u 2` for C++ versions and `-t 2` for JAVA versions)
                        [required]
  -alter NEWICK         Show the tree (e.g. a timetree) instead of the ASTRAL tree (their topologies MUST be identical)
                        [default=None]
  -g NEWICK, -genetrees NEWICK
                        gene trees for branch lengths in TEST mode [default=None]

Tree options:

  -align                Align tips [default=False]
  -cp, -concordance_percent
                        Show gene-species trees concordance percent at inner nodes instead of PP [default=False]
  -branch_size BRANCH_SIZE
                        Font size of text in branch [default=48]
  -leaf_size LEAF_SIZE  Font size of leaf name [default=60]

Barcharts options:

  -sort                 Sort q1, q2 and q3, which will miss the directionality [default=False]
  -notext               Do not draw text on the barcharts [default=False]
  -figsize FIGSIZE      Figure size of barcharts [default=3]
  -fontsize FONTSIZE    Font size of text in barcharts [default=13]
  -figfmt FIGFMT        Figure format of barcharts in tmpdir [default=png]
  -polytomy_test        Test for polytomies [default=False]

Piecharts options:

  -pie, -pie_chart      Use piechart instead of barchart [default=False]
  -pie_size PIE_SIZE    Size of Piecharts [default=30]
  -pie_fold PIE_FOLD    Fold of font size between Barcharts and Piecharts [default=6]
  -bl                   Branch lengths to check [default=False]

Branch length (BL) options:

Test mode:

  -test [TAXON/FILE [TAXON/FILE ...]]
                        Test four-taxon (the first is outgroup and others are sampled for three ingroups) [default=None]
  -astral_bin STR       ASTRAL command ('astral-pro', 'astral-hybrid', ...) [default=astral-pro]
  -outgroup STR         Outgroup [default: the first of `-test`]

Clade operateion:

  -clades FILE          Difinition of clades [default=None]
  -collapse [TAXON/FILE [TAXON/FILE ...]]
                        Collapse clades [default=None]
  -onshow TAXON/FILE [TAXON/FILE ...]
                        Only show charts on these inner nodes [default=None]
  -noshow TAXON/FILE [TAXON/FILE ...]
                        Don't show charts on these inner nodes [default=None]
  -subset TAXON/FILE [TAXON/FILE ...]
                        Show a subset clade with their MCRA [default=None]

Output:

  -pre STR, -prefix STR
                        Prefix for output [default=None]
  -tmp DIR, -tmpdir DIR
                        Temporary directory [default=tmp]

Visual parameters for adjusting graph output:

1. Get barcharts with different colors:

phytop astral.tree -colors red,yellow,black

Figure. Visual result of Phytop on example data with "-colors" parameter. Set the columns to different colors

2. Resize barplot and text:

phytop astral.tree -figsize 1 -fontsize 4

Figure. Visual result of Phytop on example data with "-figsize" and "-fontsize" parameters. "-figsize 1 -fontsize 4" in this example. These parameters can be used to adjust the image size and font size of the barplots.

3. Get piecharts:

phytop astral.tree -pie -cp

Figure. Visual result of Phytop on example data with "-pie -cp" parameters. In the pie chart, only the proportions of the q1 topologies are shown

4. Resize the pieplot size:

phytop astral.tree -pie -pie_size 20

Figure. Visual result of Phytop on example data with "-pie_size". "-pie -pie_size 20" in this example. This parameter can be used to adjust font size of of piecharts.

5. Get barcharts with collapse for clades:

phytop astral.tree -clades setcladefile -collapse

Figure. Visual result of Phytop on example data with collapse for clades. Juglans regia and Juglans sigillata were collepse for Juglans1

6. Get barcharts displays a selection of nodes:

phytop astral.tree -clades setcladefile -onshow Juglans1

Figure. Visual result of Phytop on example data with a subset of nodes. Only the information about the specified node is displayed

7. Get barcharts displays a selection of nodes:

phytop astral.tree -clades setcladefile -noshow Juglans1

Figure. Visual result of Phytop on example data with specified node information not displayed. The information about the specified node is not displayed

Visual parameters for adjusting fonts:

1. Adjust the leaf size:

phytop astral.tree -leaf_size 20

Figure. Visual result of Phytop on example data with "-leaf_size". "-leaf_size 20" in this example. This parameter can be used to adjust font size of font size of leaf names.

2. Adjust the font size of branch size:

phytop astral.tree -branch_size 20

Figure. Visual result of Phytop on example data with "-branch_size" parameter. "-branch_size 20" in this example. This parameter can be used to adjust font size of text in branch.

3. Make barplot not display text:

phytop astral.tree -notext

Figure. Visual result of Phytop on example data with "-notext" parameter. Use this parameter to make the text of the barplots not display.

Visual parameters for adjusting clades:

1. Customizing the location of lineages:

phytop astral.tree -align

Figure. Visual result of Phytop on example data with "-align" parameter. This parameter can be used to make leaf names aligned.

2. Select part of the lineages to show:

phytop astral.tree -subset Juglans_nigra Juglans_sigillata Juglans_regia

Figure. Visual result of Phytop on example data with "-branchsize" parameter. "-branchsize 20" in this example. This parameter can be used to select subset of leaves.