Topological Distance Research Articles

Spectral cluster supertree: fast and statistically robust merging of rooted phylogenetic trees.

The algorithms for phylogenetic reconstruction are central to computational molecular evolution. The relentless pace of data acquisition has exposed their poor scalability and the conclusion that the conventional application of these methods is impractical and not justifiable from an energy usage perspective. Furthermore, the drive to improve the statistical performance of phylogenetic methods produces increasingly parameter-rich models of sequence evolution, which worsens the computational performance. Established theoretical and algorithmic results identify supertree methods as critical to divide-and-conquer strategies for improving scalability of phylogenetic reconstruction. Of particular importance is the ability to explicitly accommodate rooted topologies. These can arise from the more biologically plausible non-stationary models of sequence evolution. We make a contribution to addressing this challenge with Spectral Cluster Supertree, a novel supertree method for merging a set of overlapping rooted phylogenetic trees. It offers significant improvements over Min-Cut supertree and previous state-of-the-art methods in terms of both time complexity and overall topological accuracy, particularly for problems of large size. We perform comparisons against Min-Cut supertree and Bad Clade Deletion. Leveraging two tree topology distance metrics, we demonstrate that while Bad Clade Deletion generates more correct clades in its resulting supertree, Spectral Cluster Supertree's generated tree is generally more topologically close to the true model tree. Over large datasets containing 10,000 taxa and 500 source trees, where Bad Clade Deletion usually takes 2 h to run, our method generates a supertree in on average 20 s. Spectral Cluster Supertree is released under an open source license and is available on the python package index as sc-supertree.

The upper bound of information diffusion in code review

BackgroundCode review, the discussion around a code change among humans, forms a communication network that enables its participants to exchange and spread information. Although reported by qualitative studies, our understanding of the capability of code review as a communication network is still limited.ObjectiveIn this article, we report on a first step towards understanding and evaluating the capability of code review as a communication network by quantifying how fast and how far information can spread through code review: the upper bound of information diffusion in code review.MethodIn an in-silico experiment, we simulate an artificial information diffusion within large (Microsoft), mid-sized (Spotify), and small code review systems (Trivago) modelled as communication networks. We then measure the minimal topological and temporal distances between the participants to quantify how far and how fast information can spread in code review.ResultsAn average code review participants in the small and mid-sized code review systems can spread information to between 72 % and 85 % of all code review participants within four weeks independently of network size and tooling; for the large code review systems, we found an absolute boundary of about 11 000 reachable participants. On average (median), information can spread between two participants in code review in less than five hops and less than five days.ConclusionWe found evidence that the communication network emerging from code review scales well and spreads information fast and broadly, corroborating the findings of prior qualitative work. The study lays the foundation for understanding and improving code review as a communication network.

On Symmetrical Convex Polytopes and their Edge Resolvability

The \textit{metric dimension} of a graph Γ = ( V , E ) , denoted by dim ( Γ ) , is the least cardinality of a set of vertices in Γ such that each vertex in Γ is determined uniquely by its vector of distances to the vertices of the chosen set. The topological distance between an edge ε = y z ∈ E and a vertex k ∈ V is defined as d ( ε , k ) = min { d ( z , k ) , d ( y , k ) } . A subset of vertices R Γ in V is called an edge resolving set for Γ if for each pair of different edges e 1 and e 2 in E , there is a vertex j ∈ R Γ such that d ( e 1 , j ) ≠ d ( e 2 , j ) . An edge resolving set with minimum cardinality is called the edge metric basis for Γ and this cardinality is the edge metric dimension of Γ , denoted by dim E ( Γ ) . In this article, we show that the cardinality of the minimum edge resolving set is three or four for two classes of convex polytopes ( S n and T n ) that exist in the literature.

A Topological Distance Between Multi-Fields Based on Multi-Dimensional Persistence Diagrams.

The problem of computing topological distance between two scalar fields based on Reeb graphs or contour trees has been studied and applied successfully to various problems in topological shape matching, data analysis, and visualization. However, generalizing such results for computing distance measures between two multi-fields based on their Reeb spaces is still in its infancy. Towards this, in the current article we propose a technique to compute an effective distance measure between two multi-fields by computing a novel multi-dimensional persistence diagram (MDPD) corresponding to each of the (quantized) Reeb spaces. First, we construct a multi-dimensional Reeb graph (MDRG), which is a hierarchical decomposition of the Reeb space into a collection of Reeb graphs. The MDPD corresponding to each MDRG is then computed based on the persistence diagrams of the component Reeb graphs of the MDRG. Our distance measure extends the Wasserstein distance between two persistence diagrams of Reeb graphs to MDPDs of MDRGs. We prove that the proposed measure is a pseudo-metric and satisfies a stability property. Effectiveness of the proposed distance measure has been demonstrated in (i) shape retrieval contest data - SHREC 2010 and (ii) Pt-CO bond detection data from computational chemistry. Experimental results show that the proposed distance measure based on the Reeb spaces has more discriminating power in clustering the shapes and detecting the formation of a stable Pt-CO bond as compared to the similar measures between Reeb graphs.

The prediction of donor number and acceptor number of electrolyte solvent molecules based on machine learning

Electrolyte solvents have a critical impact on the design of high performance and safe batteries. Gutmann’s donor number (DN) and acceptor number (AN) values are two important parameters to screen and design superior electrolyte solvents. However, it is more time-consuming and expensive to obtain DN and AN values through experimental measurements. Therefore, it is essential to develop a method to predict DN and AN values. This paper presented the prediction models for DN and AN based on molecular structure descriptors of solvents, using four machine learning algorithms such as CatBoost (Categorical Boosting), GBRT (Gradient Boosting Regression Tree), RF (Random Forest) and RR (Ridge Regression). The results showed that the DN and AN prediction models based on CatBoost algorithm possesses satisfactory prediction ability, with R2 values of the testing set are 0.860 and 0.96. Moreover, the study analyzed the molecular structure parameters that impact DN and AN. The results indicated that TDB02m (3D Topological distance based descriptors−lag 2 weighted by mass) had a significant effect on DN, while HATS1s (leverage-weighted autocorrelation of lag 1/weighted by I-state) plays an important role in AN. The work provided an efficient approach for accurately predicting DN and AN values, which is useful for screening and designing electrolyte solvents.

From molecular descriptors to the developmental toxicity prediction of pesticides/veterinary drugs/bio-pesticides against zebrafish embryo: Dual computational toxicological approaches for prioritization

The escalating introduction of pesticides/veterinary drugs into the environment has necessitated a rapid evaluation of their potential risks to ecosystems and human health. The developmental toxicity of pesticides/veterinary drugs was less explored, and much less the large-scale predictions for untested pesticides, veterinary drugs and bio-pesticides. Alternative methods like quantitative structure-activity relationship (QSAR) are promising because their potential to ensure the sustainable and safe use of these chemicals. We collected 133 pesticides and veterinary drugs with half-maximal active concentration (AC50) as the zebrafish embryo developmental toxicity endpoint. The QSAR model development adhered to rigorous OECD principles, ensuring that the model possessed good internal robustness (R2 > 0.6 and QLOO2 > 0.6) and external predictivity (Rtest2 > 0.7, QFn2 >0.7, and CCCtest > 0.85). To further enhance the predictive performance of the model, a quantitative read-across structure-activity relationship (q-RASAR) model was established using the combined set of RASAR and 2D descriptors. Mechanistic interpretation revealed that dipole moment, the presence of C-O fragment at 10 topological distance, molecular size, lipophilicity, and Euclidean distance (ED)-based RA function were main factors influencing toxicity. For the first time, the established QSAR and q-RASAR models were combined to prioritize the developmental toxicity of a vast array of true external compounds (pesticides/veterinary drugs/bio-pesticides) lacking experimental values. The prediction reliability of each query molecule was evaluated by leverage approach and prediction reliability indicator. Overall, the dual computational toxicology models can inform decision-making and guide the design of new pesticides/veterinary drugs with improved safety profiles.

Stepwise Functional Brain Architecture Correlates with Atrophy in Progressive Supranuclear Palsy.

Stepwise functional connectivity (SFC) detects whole-brain functional couplings of a selected region of interest at increasing link-step topological distances. This study applied SFC to test the hypothesis that stepwise architecture propagating from the disease epicenter would shape patterns of brain atrophy in patients with progressive supranuclear palsy-Richardson's syndrome (PSP-RS). Thirty-six patients with PSP-RS and 44 age-matched healthy control subjects underwent brain magnetic resonance imaging on a 3-T scanner. The disease epicenter was defined as the peak of atrophy observed in an independent cohort of 13 cases with postmortem confirmation of PSP pathology and used as seed region for SFC analysis. First, we explored SFC rearrangements in patients with PSP-RS, as compared with age-matched control subjects. Subsequently, we tested SFC architecture propagating from the disease epicenter as a determinant of brain atrophy distribution. The disease epicenter was identified in the left midbrain tegmental region. Compared with age-matched control subjects, patients with PSP-RS showed progressively widespread decreased SFC of the midbrain with striatal and cerebellar regions through direct connections and sensorimotor cortical regions through indirect connections. A correlation was found between average link-step distance from the left midbrain in healthy subjects and brain volumes in patients with PSP-RS (r = 0.38, P < 0.001). This study provides comprehensive insights into the topology of functional network rearrangements in PSP-RS and demonstrates that the brain architectural topology, as described by SFC propagating from the disease epicenter, shapes the pattern of atrophic changes in PSP-RS. Our findings support the view of a network-based pathology propagation in this primary tauopathy. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

One chiral fingerprint to find them all

Molecular fingerprints are indispensable tools in cheminformatics. However, stereochemistry is generally not considered, which is problematic for large molecules which are almost all chiral.Herein we report MAP4C, a chiral version of our previously reported fingerprint MAP4, which lists MinHashes computed from character strings containing the SMILES of all pairs of circular substructures up to a diameter of four bonds and the shortest topological distance between their central atoms. MAP4C includes the Cahn-Ingold-Prelog (CIP) annotation (R, S, r or s) whenever the chiral atom is the center of a circular substructure, a question mark for undefined stereocenters, and double bond cis–trans information if specified. MAP4C performs slightly better than the achiral MAP4, ECFP and AP fingerprints in non-stereoselective virtual screening benchmarks. Furthermore, MAP4C distinguishes between stereoisomers in chiral molecules from small molecule drugs to large natural products and peptides comprising thousands of diastereomers, with a degree of distinction smaller than between structural isomers and proportional to the number of chirality changes. Due to its excellent performance across diverse molecular classes and its ability to handle stereochemistry, MAP4C is recommended as a generally applicable chiral molecular fingerprint.Scientific contribution The ability of our chiral fingerprint MAP4C to handle stereoisomers from small molecules to large natural products and peptides is unprecedented and opens the way for cheminformatics to include stereochemistry as an important molecular parameter across all fields of molecular design.Graphical

Position-aware compositional embeddings for compressed recommendation systems

GNN recommendation models like NGCF (Wang et al., 2019), LightGCN (He et al., 2020), map each user/item to a unique embedding vector by an embedding table as input features, and then learn further their representations by leveraging multi-hop neighbors on the bipartite graph. In real world, the embedding layer incurs gigabytes of memory consumption for hundreds of thousands of users and items, which is difficult to be deployed due to a plethora of engineering challenges. There are different methods to reduce the size of an embedding table. However, most hashing-based models fail to capture graph-structure information and keep topological distance for users/items in the compressed embedding space. To this end, we present Position-aware Compositional Embedding (PCE) as a low-memory alternative to the embedding layer. PCE constructs unique embedding for each user/item by combining fixed-size anchor nodes and its attached co-cluster on the graph. PCE incorporates global and co-cluster positions into compositional embeddings, obtaining competitive representation capability in the compressed case. Extensive experiments on three recommendation graphs demonstrate that our PCE exceeds state-of-the-art compression techniques. In particular, compared with complete embedding table schema, PCE has a ∼5% relative loss in Recall@20 averagely and 16x fewer parameters. Moreover, our model can be compressed by 2x while getting even better accuracy.

Predicting the Time-Dependent Toxicities of Binary Mixtures of Five Antibiotics to Vibrio qinghaiensis sp.-Q67 Based on the QSAR Model.

Antibiotics may be exposed in a mixed state in natural environments. The toxicity of antibiotic mixtures exhibits time-dependent characteristics, and data on the time-dependent toxicity of antibiotic mixtures is also relatively lacking. In this study, the toxicities of 45 binary mixtures composed of five antibiotics were investigated against Vibrio qinghaiensis sp.-Q67 (Q67) at multiple exposure times (4, 6, 8, 10, and 12 h). Quantitative structure-activity relationship (QSAR) models were developed for predicting the time-dependent toxicities of 45 binary mixtures. The results showed that the best QSAR models presented coefficient of determination (R 2) of (0.818-0.913) and explained variance in prediction leave-one-out (Q 2 LOO) of (0.781-0.894) and predictive ability (Q 2 F1, Q 2 F2, Q 2 F3 > 0.682, concordance correlation coefficient > 0.859). The R 2 values of QSAR models outperformed the R 2 (0.628-0.810) of the conventional concentration addition models and the R 2 (0.654-0.792) of the independent action models. Furthermore, the QSAR models showed higher R 2 and Q 2 LOO values at 4 h compared to other exposure times. Specifically, the model at the 30% effective concentration (EC30) had R 2 of 0.902 and Q 2 LOO of 0.883, while the model at the 50% effective concentration (EC50) had R 2 of 0.913 and Q 2 LOO of 0.894. The CATS2D_04_DP descriptor was found to be the most dominant and negatively correlated factor influencing the toxicity of mixed antibiotics against Q67 in the nine QSAR models developed over five exposure times. The reduction in the number of DP pharmacophore point pairs with a topological distance of 4 in the represented molecules is the primary cause for the rise in the time-dependent toxicity of the antibiotics against Q67.

Structure-Activity Relationship Studies on VEGFR2 Tyrosine Kinase Inhibitors for Identification of Potential Natural Anticancer Compounds.

Over-expression of Vascular Endothelial Growth Factor Receptors (VEGFRs) leads to the hyperactivation of oncogenes. For inhibition of this hyperactivation, the USA Food Drug Administration (FDA) has approved many drugs that show adverse effects, such as hypertension, hypothyroidism, etc. There is a need to discover potent natural compounds that show minimal side effects. In the present study, we have taken structurally diverse known VEGFR2 inhibitors to develop a Quantitative Structure-Activity Relationship (QSAR) model and used this model to predict the inhibitory activity of natural compounds for VEGFR2. The QSAR model was developed through the forward stepwise Multiple Linear Regression (MLR) method. A developed QSAR model was used to predict the inhibitory activity of natural compounds. Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) assessment and molecular docking studies were performed. The binding stability of the natural compounds with VEGFR2 was elucidated through Molecular Dynamics (MD) simulation. The developed QSAR model against VEGFR2 showed the regression coefficient of the training dataset (r2) as 0.81 and the external regression coefficient of the test dataset (r2 test) 0.71. Descriptors, viz., electro-topological state of potential hydrogen bonds (maxHBint2, nHBint6), atom types (minssNH), maximum topological distance matrix (SpMAD_Dt), and 2D autocorrelation (ATSC7v), have been identified. Using this model, 14 natural compounds have been selected that have shown inhibitory activity for VEGFR2, of which six natural compounds have been found to possess a strong binding affinity with VEGFR2. In MD simulation, four complexes have shown binding stability up to 50ns. The developed QSAR model has identified 5 conserved activity-inducing physiochemical properties, which have been found to be correlated with the anticancer activity of the nonidentical ligand molecules bound with the VEGFR2 kinase. Lavendustin_A, 3'-O-acetylhamaudol, and arctigenin have been obtained as possible lead natural compounds against the VEGFR2 kinase.

Trade fragmentation and volatility-of-volatility networks

We assess the impact of trade fragmentation in equity markets using volatility networks following the volatility-of-volatility (VoV) approach. VoV networks offer an original method for measuring and visualizing the common component of volatilities. We use topological distance and connectivity indicators describing their structure as alternative proxies of VoV. Further, we use panel tests to apply threshold effects regression models on French equity market data after the introduction of MiFID, both at portfolio level and asset level. We show that market fragmentation yields a reduction in VoV, corresponding to both a contraction of volatility networks and a change in their structure. This effect strengthens in the stabilizing fragmentation regime compared to the increased fragmentation regime. Since VoV has been shown to predict stock markets returns, this original finding is widely relevant to market operators, regulators and public authorities.

Select Your Own Counterparts: Self-Supervised Graph Contrastive Learning With Positive Sampling.

Contrastive learning (CL) has emerged as a powerful approach for self-supervised learning. However, it suffers from sampling bias, which hinders its performance. While the mainstream solutions, hard negative mining (HNM) and supervised CL (SCL), have been proposed to mitigate this critical issue, they do not effectively address graph CL (GCL). To address it, we propose graph positive sampling (GPS) and three contrastive objectives. The former is a novel learning paradigm designed to leverage the inherent properties of graphs for improved GCL models, which utilizes four complementary similarity measurements, including node centrality, topological distance, neighborhood overlapping, and semantic distance, to select positive counterparts for each node. Notably, GPS operates without relying on true labels and enables preprocessing applications. The latter aims to fuse positive samples and enhance representative selection in the semantic space. We release three node-level models with GPS and conduct extensive experiments on public datasets. The results demonstrate the superiority of GPS over state-of-the-art (SOTA) baselines and debiasing methods. In addition, the GPS has also been proven to be versatile, adaptive, and flexible.

The first report on the assessment of maximum acceptable daily intake (MADI) of pesticides for humans using intelligent consensus predictions.

Direct or indirect consumption of pesticides and their related products by humans and other living organisms without safe dosing may pose a health risk. The risk may arise after a short/long time which depends on the nature and amount of chemicals consumed. Therefore, the maximum acceptable daily intake of chemicals must be calculated to prevent these risks. In the present work, regression-based quantitative structure-activity relationship (QSAR) models were developed using 39 pesticides with maximum acceptable daily intake (MADI) for humans as the endpoint. From the statistical results (R2 = 0.674-0.712, QLOO2 = 0.553-0.580, Q(F1)2 = 0.544-0.611, and Q(F2)2 = 0.531-0.599), it can be inferred that the developed models were robust, reliable, reproducible, accurate, and predictive. Intelligent Consensus Prediction (ICP) was employed to improve the external predictivity (Q(F1)2 =0.579-0.657 and Q(F2)2 = 0.563-0.647) of the models. Some of the chemical markers responsible for toxicity enhancement are the presence of unsaturated bonds, lipophilicity, presence of C< (double bond-single bond-single bonded carbon), and the presence of sulphur and phosphate bonds at the topological distances 1 and 6, while the presence of hydrophilic groups and short chain fragments reduces the toxicity. The Pesticide Properties Database (PPDB) (1694 pesticides) was also screened with the developed models. Hence, this research work will be helpful for the toxicity assessment of pesticides before their synthesis, the development of eco-friendly and safer pesticides, and data-gap filling reducing the time, cost, and animal experimentation. Thus, this study might hold promise for future potential MADI assessment of pesticides and provide a meaningful contribution to the field of risk assessment.

The role of street network metrics in shaping distance distributions in a residential neighbourhood

Walkability studies often rely on physical proximity metrics for destination accessibility. However, some recent studies argue that configuration (topological) distance provides a more accurate reflection of the actual distances experienced by individuals. This study therefore aims to test the extent to which an association exists between network-metric proximity to several destinations and two main measures of space syntax – integration and choice – in a dendriform network structure such as Putrajaya city (Malaysia). Using GIS, multiple buffer-service areas were generated around each housing unit (N = 2,392). Interpolation and space syntax analyses were conducted to assess metric and topological distance at local and global levels for each buffer. The statistical analysis showed that distances to commercial areas, transportation and average distances to all destinations were strongly affected by the syntactical properties of the neighbourhood. Moreover, global measures were more powerful in detecting metric-distance changes compared to local measures. Aligned with natural movement theory, these results support the idea that the spatial properties of urban form have a significant impact on distance distributions within residential settings, specifically distances to commercial areas. Therefore, policies that promote mixed-use development, especially in areas with good transportation access, should consider the impact of syntactical accessibility of the network.

A unified framework for backpropagation-free soft and hard gated graph neural networks

We propose a framework for the definition of neural models for graphs that do not rely on backpropagation for training, thus making learning more biologically plausible and amenable to parallel implementation. Our proposed framework is inspired by Gated Linear Networks and allows the adoption of multiple graph convolutions. Specifically, each neuron is defined as a set of graph convolution filters (weight vectors) and a gating mechanism that, given a node and its topological context, generates the weight vector to use for processing the node’s attributes. Two different graph processing schemes are studied, i.e., a message-passing aggregation scheme where the gating mechanism is embedded directly into the graph convolution, and a multi-resolution one where neighboring nodes at different topological distances are jointly processed by a single graph convolution layer. We also compare the effectiveness of different alternatives for defining the context function of a node, i.e., based on hyperplanes or on prototypes, and using a soft or hard-gating mechanism. We propose a unified theoretical framework allowing us to theoretically characterize the proposed models’ expressiveness. We experimentally evaluate our backpropagation-free graph convolutional neural models on commonly adopted node classification datasets and show competitive performances compared to the backpropagation-based counterparts.

Epileptogenic networks in extra temporal lobe epilepsy.

Extra temporal lobe epilepsy (eTLE) may involve heterogenous widespread cerebral networks. We investigated the structural network of an eTLE cohort, at the postulated epileptogenic zone later surgically removed, as a network node: the resection zone (RZ). We hypothesized patients with an abnormal connection to/from the RZ to have proportionally increased abnormalities based on topological proximity to the RZ, in addition to poorer post-operative seizure outcome. Structural and diffusion MRI were collected for 22 eTLE patients pre- and post-surgery, and for 29 healthy controls. The structural connectivity of the RZ prior to surgery, measured via generalized fractional anisotropy (gFA), was compared with healthy controls. Abnormal connections were identified as those with substantially reduced gFA (z < -1.96). For patients with one or more abnormal connections to/from the RZ, connections with closer topological distance to the RZ had higher proportion of abnormalities. The minority of the seizure-free patients (3/11) had one or more abnormal connections, while most non-seizure-free patients (8/11) had abnormal connections to the RZ. Our data suggest that eTLE patients with one or more abnormal structural connections to/from the RZ had more proportional abnormal connections based on topological distance to the RZ and associated with reduced chance of seizure freedom post-surgery.

A Security Scheme for Statistical Anomaly Detection and the Mitigation of Rank Attacks in RPL Networks (IoT Environment)

A Routing Protocol for Low-power-lossy (RPL) networks builds a Destination Oriented Directed Acyclic Graph (DODAG) to provide IPv6 connectivity for resource-constrained devices over a large variety of low-power-lossy link layer technologies. Each RPL node maintains a rank value, which quantizes its relative topological distance from the DODAG root and is calculated based on the rank of its preferred parents and the objective function being employed. The RPL routing process does not impose any check to monitor the action and conduct of the parent nodes. A malicious attacking node can exploit this weakness by faking its rank value to be much lower than the original to attract more traffic to traverse through it from its neighboring and underlying child nodes. An attacking node can choose to perform selective forwarding or a sinkhole attack (Rank Attack type 1 – RA1) or exacerbate network performance parameters by causing topological instability (Rank Attack type 2 - RA2). This paper presents the Statistically-based Anomaly Detection Scheme (SARPL) to detect RA1 and RA2 and attempts to mitigate their effects. The simulations and performance evaluations show that SARPL can successfully detect RA1 attacks in all scenarios whereas it has a positive detection rate of approximately 93% for RA2 type attacks. SARPL also significantly improves network performance parameters, such as packet delivery rate and end-to-end delay, while mitigating the effects of RA1 and RA2.

Differentiate data by higher-order structures

The comparison of two objects is a topic that exists widely in different research areas. In this study, the network distance is combined with the k-nearest neighbour network sequence to construct the topological structural distance (TSD). This indicator is used to quantitatively describe the difference between two sets of points in any metric structure. Several datasets were tested to demonstrate the effectiveness of this indicator. Calculations show that TSD can compare the intrinsic structure of low-dimensional and high-dimensional datasets and is not limited by dimension. In addition, TSD can also be used to characterize sets of points in discrete space, such as comparing the structure of different networks. The examples in this study show that TSD is a universal method for analyzing the intrinsic structure of data.

EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets

BackgroundGenome-scale phylogenetic analysis based on core gene sets is routinely used in microbiological research. However, the techniques are still not approachable for individuals with little bioinformatics experience. Here, we present EasyCGTree, a user-friendly and cross-platform pipeline to reconstruct genome-scale maximum-likehood (ML) phylogenetic tree using supermatrix (SM) and supertree (ST) approaches.ResultsEasyCGTree was implemented in Perl programming languages and was built using a collection of published reputable programs. All the programs were precompiled as standalone executable files and contained in the EasyCGTree package. It can run after installing Perl language environment. Several profile hidden Markov models (HMMs) of core gene sets were prepared in advance to construct a profile HMM database (PHD) that was enclosed in the package and available for homolog searching. Customized gene sets can also be used to build profile HMM and added to the PHD via EasyCGTree. Taking 43 genomes of the genus Paracoccus as the testing data set, consensus (a variant of the typical SM), SM, and ST trees were inferred via EasyCGTree successfully, and the SM trees were compared with those inferred via the pipelines UBCG and bcgTree, using the metrics of cophenetic correlation coefficients (CCC) and Robinson–Foulds distance (topological distance). The results suggested that EasyCGTree can infer SM trees with nearly identical topology (distance < 0.1) and accuracy (CCC > 0.99) to those of trees inferred with the two pipelines.ConclusionsEasyCGTree is an all-in-one automatic pipeline from input data to phylogenomic tree with guaranteed accuracy, and is much easier to install and use than the reference pipelines. In addition, ST is implemented in EasyCGTree conveniently and can be used to explore prokaryotic evolutionary signals from a different perspective. The EasyCGTree version 4 is freely available for Linux and Windows users at Github (https://github.com/zdf1987/EasyCGTree4).