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PhyloTracer: A Versatile Toolkit for Comparative Genomics and Phylogenomics Analysis.
Pypi: https://pypi.org/project/PhyloTracer
Github: https://github.com/YiyongZhao/PhyloTracer
Licence: MIT license
Release Date: 2023-7
Contacts: Taoli([email protected]); Yiyong Zhao([email protected])
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A User-Friendly Toolkit for Comprehensive inference for the Manipulation of Tree Format, Gene Tree Rooting, the Origin and Loss of Gene Duplication Events, Ortholog Retrieval, Phylogenetic Noise Elimination, Gene Tree Topology Summary, Species Hybridization Detection, and Visualization.
PhyloTracer aims to provide more accurate rooting of gene trees, serving as a foundation for inferring putative orthologous genes. It also includes functions to statistically summarize the topology types for models like ABAB-ABBA, aiding in identifying hybridization signals.
- PhyloTree_CollapseExpand: To transform a phylogenetic tree with Newick format into a ‘comb’ structure based on a predefined support value threshold. It can also revert the 'comb' structure to the binary tree, allowing meet the standard software analysis requirements.
- PhyloSupport_Scaler: To recalibrate support values (bootstrap/posterior probability) for a phylogenetic tree, scaling them between [0,1] and [1,100] ranges for computational requirements.
- BranchLength_NumericConverter: To convert values of branch length with string format to numeric format for a phylogenetic tree, critical for quantitative analysis and computational operations.
- Phylo_Rooter: Enables an accuracy method for gene tree rooting and enhancing the downstream evolutionary genomic analysis.
- OrthoFilter_LB: To prune phylogenomic noises from single-copy and multi-copy gene family trees by removing the tips with long branch lengths.
- OrthoFilter_Mono: To prune phylogenomic noise from single-copy and multi-copy gene family trees. It removes outliers and paralogs based on predefined taxonomic constraints (e.g., ensuring members from taxa such as families or orders form monophyletic groups). Caution: Groupings should be selected with care, prioritizing well-established relationships unless otherwise required for specific objectives.
- TreeTopology_Summarizer: To enumerate the frequency of both absolute and relative topologies for single-copy gene trees or interested predefined clades.
- Tree_Visualizer: To visualize and integrate gene duplication detection results into the species tree.
- GD_Detector: To identify gene duplication events by reconciliation of gene family trees to a species tree.
- GD_Visualizer: To visualize gene duplication detection on the context of a species tree.
- GD_Loss_Tracker: To track the gene duplication loss event starting across each nodes/tips from a specific GD burst event in the species tree.
- GD_Loss_Visualizer: To visualize the summary of gene duplication loss event counts for each nodes/tips on the context of the species tree.
- Ortho_Retriever: To rapid infer putative single-copy orthologs by splitting paralogs from large-scale gene family trees across multiple species.
- Hybrid_Tracer: To detect hybridization signals for each potential GD burst event across species tree by using the D-statistic (ABAB-BABA) test.
- Hybrid_Visualizer: To visualize hybridization signals, highlighting support from gene tree topologies and D-statistic signals.
- HaploFinder: Distinguishing ancient genome recombination events including gene conversions and crossovers by tracing subgenome haplotypes through phylogenomic profiling.
#A convenient one-click installation by using conda (https://docs.conda.io/projects/conda/en/stable/user-guide/install/index.html) with the following commands:
git clone https://github.com/YiyongZhao/PhyloTracer.git
cd PhyloTracer
conda env create -f environment.yml
conda activate phylotracer
#Alternatively, a convenient one-click installation by using pip (the package installer for Python) with the following commands:
chmod +x install_packages.sh
bash install_package.sh
#Reminder for potential visualization issues: qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found and this application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
#Alternative available platform plugins include: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-#egl, wayland-xcomposite-glx, webgl, xcb. before running PhyloTracer, please execute the following bash command:
export QT_QPA_PLATFORM=linuxfbpip install PhyloTracer- Incorporating the principles of maximizing the outgroup depth score, minimizing the Robinson-Foulds (RF) distance, reducing the variance in ingroup branch lengths, and maximizing the overlap ratio of gene duplication species enhances the accuracy of root determination.
- Introducing the concept of long-branch genes for noise filtration in gene trees.
- Introducing the concept of inserted genes for monophyletic filtering in single-copy gene trees.
- Python 3.0+
- Python modules:
- ete3
- HyDe
- pandas
- numpy
- tqdm
- time
- pypdf4
- matplotlib
- pyqt5
Note: PhyloTracer uses basic functions of analysis and visualization of trees from Python framework ete3 and detects species hybridization signals using ABAB-BABA test by HyDe.
The following input file should have two columns and be separated by a tab key.
------------GF_ID2path.imap--------------------------------------------------------------------------------------------------------
OG_104001 example_data/Phylo_Rooter/OG_104001.treefile
OG_104002 example_data/Phylo_Rooter/OG_104002.treefile
OG_104003 example_data/Phylo_Rooter/OG_104003.treefile
------------gene2length.imap---------------------------------------------------------------------------------------------------
AMTR_s00796p00010580 201
ATCG00500.1 1467
Glyma.07G273800.2 3417
------------gene2sps.imap #should sorted by second column with the recommended bash command: sort -k2,2 gene2sps.imap-------------------
AMTR_s00796p00010580 Amborella_trichopoda
ATCG00500.1 Arabidopsis_thaliana
Glyma.07G273800.2 Glycine_max
------------gene2family.imap------------------------------------------------------------------------------------------------------
AMTR_s00796p00010580 Amborellaceae
ATCG00500.1 Brassicaceae
Glyma.07G273800.2 Fabaceae
------------gene2order.imap--------------------------------------------------------------------------------------------------------
AMTR_s00796p00010580 Amborellales
ATCG00500.1 Brassicales
Glyma.07G273800.2 Fabales
------------gene2taxa.imap--------------------------------------------------------------------------------------------------------
AMTR_s00796p00010580 Angiosperm
ATCG00500.1 Malvids
Glyma.07G273800.2 Fabids
------------gene2clade.imap--------------------------------------------------------------------------------------------------------
AMTR_s00796p00010580 Nitrogen-fixing
ATCG00500.1 Nitrogen-fixing
Glyma.07G273800.2 non-Nitrogen-fixing
------------gene2expression.imap---------------------------------------------------------------------------------------------------
AMTR_s00796p00010580 5.0
ATCG00500.1 12.0
Glyma.07G273800.2 0.0
#Note: You can add any number of imap files. They will sequentially provide annotations to the right of the gene tips according to the order of input.
Description:
To transform a phylogenetic tree in Newick format into a 'comb' structure based on a predefined support value threshold. It can also revert this `comb` structure to a fully resolved binary tree, allowing dynamic topology adjustments
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--support_value Nodes whose support is less than or equal to 'support_value' will be converted
Optional parameter:
--revert Revert this 'comb' structure to a fully resolved binary tree
Usage:
Phylo_Tracer.py PhyloTree_CollapseExpand --input_GF_list GF_ID2path.imap --support_value 50 [--revert]
Description:
To recalibrate support value from bootstrap or posterior probability in a phylogenetic tree, scaling them between [0,1] and [1,100] ranges for computational compatibility, and vice versa to meet various analytical needs
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--scale_to Input '1' to scale support values from 1-100 to 0-1, or '100' to scale from 0-1 to 1-100
Usage:
Phylo_Tracer.py PhyloSupport_Scaler --input_GF_list GF_ID2path.imap --scale_to 1
Description:
To convert branch length values of a phylogenetic tree from string to numerical format
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
Optional parameter:
--decimal_place Return the branch length values to 10 decimal places and default = 10
Usage:
Phylo_Tracer.py BranchLength_NumericConverter --input_GF_list GF_ID2path.imap [--decimal_place 10]
Description:
Enables an accurate method for gene tree rooting and enhancing the downstream evolutionary genomic analysis
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_imap File with classification information of species corresponding to genes
--input_gene_length File with information corresponding to gene lengths
--input_sps_tree A species tree file with Newick format
Usage:
Phylo_Tracer.py Phylo_Rooter --input_GF_list GF_ID2path.imap --input_imap gene2sps.imap --input_gene_length gene2length.imap --input_sps_tree sptree.nwk
Description:
To prune phylogenomic noises from both single-copy and multi-copy gene family trees by removing the tips with long branch length
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_imap File with classification information of species corresponding to genes
--absolute_branch_length Absolute branch length multiplier and default = 5
--relative_branch_length Relative branch length multiplier and default = 2.5
Optional parameter:
--visual Visualize the results of gene family trees before and after removing long branches
Usage:
Phylo_Tracer.py OrthoFilter_LB --input_GF_list GF_ID2path.imap --input_imap gene2sps.imap --absolute_branch_length 5 --relative_branch_length 2.5 [--visual]
Description:
To prune phylogenomic noise from both single-copy and multi-copy gene family trees. It removes outliers and paralogs based on predefined taxonomic constraints (e.g., ensuring members from taxa such as families or orders form monophyletic groups). Caution: Groupings should be selected with care, prioritizing well-established relationships unless otherwise required for specific objectives
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_taxa File with taxonomic information for species
--input_imap File with classification information of species corresponding to genes
--branch_length_multiples Tips whose branch length is greater than or equal to the branch length multiples will be removed
--insert_branch_index Nodes with insertion coverage ratio and insertion depth greater than or equal to the insert branch index will be removed
Optional parameter:
--visual Visualize the results of gene family trees before and after removing outliers and paralogs
Usage:
Phylo_Tracer.py OrthoFilter_Mono --input_GF_list GF_ID2path.imap --input_imap gene2sps.imap --input_taxa gene2clade.imap --branch_length_multiples 10 --insert_branch_index 10 [--visual]
Description:
To enumerate the frequency of both absolute and relative topologies for single-copy gene trees or interested predefined clades
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_imap File with classification information of species corresponding to genes
Usage:
Phylo_Tracer.py TreeTopology_Summarizer --input_GF_list GF_ID2path.imap --input_imap gene2sps.imap
Description:
To mark tips of gene trees with provided tags, identify GD nodes, and integrate gene duplication results onto the species tree
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_imap File with classification information of species corresponding to genes
--keep_branch 1 or 0 indicates whether or not to preserve branch length information
--tree_style The tree style, 'r' is meaning rectangular, 'c' is meaning circular
Optional parameter:
--species_categories File with taxonomic information for species
--gene_family If you want to mark gene families you need to provide this file
--input_sps_tree If you provide the --gene_family parameter, you should provide a species tree file with Newick format
--gene_expression Gene expression level files
Usage:
Phylo_Tracer.py Tree_Visualizer --input_GF_list GF_ID2path.imap --input_imap gene2sps.imap [--species_categories [gene2sps.imap gene2order.imap gene2taxa.imap gene2clade.imap] --keep_branch {1,0} --tree_style {r,c} --gene_family gene2family.imap --input_sps_tree sptree.nwk --gene_expression gene2expression.imap]
Description:
To identify gene duplication events by reconciling gene trees and species tree
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_imap File with classification information of species corresponding to genes
--gd_support GD node support [50-100]
--subclade_support The subclade support of GD node [0-100]
--dup_species_proportion The proportion of overlappped species from two subclade for a GD event with range [0-1] and default = 0.2
--dup_species_num The number of species with species duplications under the GD node
--input_sps_tree A species tree file with Newick format
--deepvar Maximum variance of deepth and default = 1
Usage:
Phylo_Tracer.py GD_Detector --input_GF_list GF_ID2path.imap --input_imap gene2sps.imap --gd_support 50 --subclade_support 50 --dup_species_proportion 0.5 --dup_species_num 1 --input_sps_tree sptree.nwk --deepvar 1
Description:
To visualize gene duplication detection results and integrate these findings onto the species tree
Required parameter:
--input_sps_tree A numbered species tree file with Newick format
--gd_result Result file of GD_Detector
Usage:
Phylo_Tracer.py GD_Visualizer --input_sps_tree sptree.nwk --gd_result gd_result.txt
Description:
To analyze and summarize gene duplication loss events traverse each node from the species tree for each tips
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_sps_tree A species tree file with Newick format
--input_imap File with classification information of species corresponding to genes
Usage:
Phylo_Tracer.py GD_Loss_Tracker --input_GF_list GF_ID2path.imap --input_sps_tree sptree.nwk --input_imap gene2sps.imap
Description:
To visualize the summary of gene duplication loss events on the context of species tree
Required parameter:
--input_folder The result folder name of GD_Loss_Tracker
--output_folder Output folder name
Usage:
Phylo_Tracer.py GD_Loss_Visualizer --input_folder input_foldername --output_folder output_foldername
Description:
To infer single-copy putative orthologs by splitting paralogs from large-scale gene family trees for multiple species
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_imap File with classification information of species corresponding to genes
--input_gene_length File with information corresponding to gene lengths
Usage:
Phylo_Tracer.py Ortho_Retriever --input_GF_list GF_ID2path.imap --input_imap gene2sps.imap --input_gene_length gene2length.imap
Description:
To use the ABAB-BABA test to detect hybridization signals for each potential GD burst event across species tree detect species hybridization events for
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_Seq_GF_list File containing paths to sequence alignment files corresponding to the gene trees
--input_imap File with classification information of species corresponding to genes
--input_sps_tree A species tree file with Newick format
Usage:
Phylo_Tracer.py Hybrid_Tracer --input_GF_list GF_ID2path.imap --input_Seq_GF_list Seq_GF_ID2path.imap --input_sps_tree sptree.nwk --input_imap gene2sps.imap
Description:
To visualize hybridization signals, highlighting support from gene tree topologies and D-statistic signals
Required parameter:
--input_hybrid_folder The result folder name of Hybrid_Tracer
--input_sps_tree A species tree file with Newick format
Usage:
Phylo_Tracer.py Hybrid_Visualizer --input_hybrid_folder input_foldername --input_sps_tree sptree.nwk
Description:
To distinguish gene conversion by tracing subgenome haplotypes through phylogenomic profiling
Required parameter:
--input_GF_list File containing paths to gene tree files, one per line
--input_imap File with classification information of species corresponding to genes
--species_a Name of species A
--species_b Name of species B
--species_a_gff GFF file of species A
--species_b_gff GFF file of species B
--species_a_lens Lens file of species A
--species_b_lens Lens file of species B
--blastp_result Blastp result between species A and species B
--synteny_result Synteny result between species A and species B
--blastp_limit Limit number of targets per gene pair in the BLASTp result
Usage:
Phylo_Tracer.py HaploFinder --input_GF_list GF.list --input_imap gene2sps.imap --species_a A --species_b B --species_a_gff A.gff --species_b_gff B.gff --species_a_lens A.lens --species_b_lens B.lens --blastp_result blastp.txt --synteny_result synteny.txt --blastp_limit 5
You can report bugs or request features through our GitHub Issues page. If you have any questions, suggestions, or issues, please do not hesitate to contact us.
If you're interested in contributing code or reporting bugs, we welcome your ideas and contributions to improve PhyloTracer! Please check out Contribution Guidelines.
Check the Changelog for details on different versions and updates.
PhyloTracer is licensed under the MIT LICENSE.
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