Tootfinder

New #preprint by Alex Koplenig and me:
"Statistical errors undermine claims about the evolution of polysynthetic languages". (#PNAS (#Linguistics

Replaced article(s) found for q-bio.PE. https://arxiv.org/list/q-bio.PE/new
[1/1]:
- PhyloProfile v2: Scalable Exploration of Multilayered Phylogenetic Profiles via Dimensionality Re...
Vinh Tran, Ingo Ebersberger

Inference of maximum parsimony phylogenetic trees with model-based classical and quantum methods
Jiawei Zhang, Yibo Chen, Yang Zhou, Jun-Han Huang
https://arxiv.org/abs/2508.00468

Inference of maximum parsimony phylogenetic trees with model-based classical and quantum methods
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design three optimization models compatible with both classical and quantum solvers. Our method directly searches the complete solution space of all possible tree topologies and ancestral states, thereby avoiding the potential biases associated with pre-constructing ca…

Asymptotic guarantees for Bayesian phylogenetic tree reconstruction
Alisa Kirichenko, Luke J. Kelly, Jere Koskela
https://arxiv.org/abs/2508.00995 https://…

Asymptotic guarantees for Bayesian phylogenetic tree reconstruction
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass several Bayesian algorithms in widespread use, such as BEAST, MrBayes, and RevBayes. Unlike essentially all existing asymptotic guarantees for tree reconstruction, we require no discretization or boundedness assumptions on branch lengths. Our results are also ve…

Brownian motion, bridges and Bayesian inference in phylogenetic tree space
William M. Woodman, Tom M. W. Nye
https://arxiv.org/abs/2506.22135 https://

Brownian motion, bridges and Bayesian inference in phylogenetic tree space
Billera-Holmes-Vogtmann (BHV) tree space is a geodesic metric space of edge-weighted phylogenetic trees with a fixed leaf set. Constructing parametric distributions on this space is challenging due to its non-Euclidean geometry and the intractability of normalizing constants. We address this by fitting Brownian motion transition kernels to tree-valued data via a non-Euclidean bridge construction. Each kernel is determined by a source tree $x_0$ (the Brownian motion's starting point) and a dispe…

Tropical cluster varieties of type C
Igor Makhlin
https://arxiv.org/abs/2508.02941 https://arxiv.org/pdf/2508.02941…

Tropical cluster varieties of type C
We explicitly describe the tropicalization of a cluster variety of finite type C, realizing it as the space of axially symmetric phylogenetic trees. We also find all occurring sign patterns of coordinates, for both the cluster variety and the cluster configuration space. We realize the corresponding signed tropicalizations as subfans of the tropicalization, with each such subfan dual to either a cyclohedron or an associahedron. As additional results, we construct Gröbner and tropical bases for…

Counting rankings of tree-child networks
Qiang Zhang, Mike Steel
https://arxiv.org/abs/2506.05730 https://arxiv.org/pdf/2506.05730

Counting rankings of tree-child networks
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are `tree-child networks' and a `ranking' of such a network is a temporal ordering of the ancestral speciation and hybridization events. In this short note, we show how to efficiently count such rankings on any given binary (or semi-binary) tree-child network. We also con…

Replaced article(s) found for math.CO. https://arxiv.org/list/math.CO/new
[2/2]:
- When are quarnets sufficient to reconstruct semi-directed phylogenetic networks?
Katharina T. Huber, Leo van Iersel, Mark Jones, Vincent Moulton, Leonie Veenema - Nipius

EvoGit: Decentralized Code Evolution via Git-Based Multi-Agent Collaboration
Beichen Huang, Ran Cheng, Kay Chen Tan
https://arxiv.org/abs/2506.02049 https:…

EvoGit: Decentralized Code Evolution via Git-Based Multi-Agent Collaboration
We introduce EvoGit, a decentralized multi-agent framework for collaborative software development driven by autonomous code evolution. EvoGit deploys a population of independent coding agents, each proposing edits to a shared codebase without centralized coordination, explicit message passing, or shared memory. Instead, all coordination emerges through a Git-based phylogenetic graph that tracks the full version lineage and enables agents to asynchronously read from and write to the evolving cod…

Replaced article(s) found for q-bio.PE. https://arxiv.org/list/q-bio.PE/new
[1/1]:
- Metrics for classes of semi-binary phylogenetic networks using $\mu$-representations
Christopher Reichling, Leo van Iersel, Yukihiro Murakami

UnMuted: Defining SARS-CoV-2 Lineages According to Temporally Consistent Mutation Clusters in Wastewater Samples
Devan Becker
https://arxiv.org/abs/2508.03508 https://

UnMuted: Defining SARS-CoV-2 Lineages According to Temporally Consistent Mutation Clusters in Wastewater Samples
SARS-CoV-2 lineages are defined according to placement in a phylogenetic tree, but approximated by a list of mutations based on sequences collected from clinical sampling. Wastewater lineage abundance is generally found under the assumption that the mutation frequency is approximately equal to the sum of the abundances of the lineages to which it belongs. By leveraging numerous samples collected over time, I am able to estimate the temporal trends of the abundance of lineages as well as the def…

On recognizing graphs representing Persistent Perfect Phylogenies
Paola Bonizzoni, Gianluca Della Vedova, Mauricio Soto Gomez, Gabriella Trucco
https://arxiv.org/abs/2507.18281 …

On recognizing graphs representing Persistent Perfect Phylogenies
The Persistent Perfect phylogeny, also known as Dollo-1, has been introduced as a generalization of the well-known perfect phylogenetic model for binary characters to deal with the potential loss of characters. The problem of deciding the existence of a Persistent Perfect phylogeny can be reduced to the one of recognizing a class of bipartite graphs whose nodes are species and characters. Thus an interesting question is solving directly the problem of recognizing such graphs. We present a polyn…

This https://arxiv.org/abs/2408.03431 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_mat…

Compactifications of phylogenetic systems and species of electrical networks
We describe new spaces and maps. Our graphical map is a visual and numerical correspondence between spaces of circular electrical networks and circular planar split systems. When restricted to the planar circular electrical case, this graphical map finds the split system uniquely associated with the Kalmanson resistance distance of the dual network, matching the induced split system familiar from phylogenetics. This correspondence is extended to compactifications of the respective spaces, takin…

Computing phylogenetic invariants for time-reversible models: from TN93 to its submodels
Marta Casanellas, Jennifer Garbett, Roser Homs, Annachiara Korchmaros, Niharika Chakrabarty Paul
https://arxiv.org/abs/2505.20526

Computing phylogenetic invariants for time-reversible models: from TN93 to its submodels
Phylogenetic invariants are equations that vanish on algebraic varieties associated with Markov processes that model molecular substitutions on phylogenetic trees. For practical applications, it is essential to understand these equations across a wide range of substitution models. Recent work has shown that, for equivariant models, phylogenetic invariants can be derived from those of the general Markov model by restricting to the linear space defined by the model (namely, the space of mixtures …

Characterizing (multi-)semi-directed phylogenetic networks
Niels Holtgrefe, Katharina T. Huber, Leo van Iersel, Mark Jones, Vincent Moulton
https://arxiv.org/abs/2507.18772 http…

Characterizing (multi-)semi-directed phylogenetic networks
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on a special class of such networks called semi-directed networks. These graphs are defined as mixed graphs that can be obtained by de-orienting some of the arcs in some rooted phylogenetic network, that is, a directed acyclic graph whose leaves correspond to a …

Phylogenetic network models as graphical models
Seth Sullivant
https://arxiv.org/abs/2507.23056 https://arxiv.org/pdf/2507.23056

Phylogenetic network models as graphical models
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree model. In particular, the concept of a local modification to a DAG model is developed and applied to the displayed tree model. As an application, some nonidentifiability issues related to the displayed tree models are highlighted as they relate to reticulation edg…

Replaced article(s) found for q-bio.GN. https://arxiv.org/list/q-bio.GN/new
[1/1]:
- Constructing Semi-Directed Level-1 Phylogenetic Networks from Quarnets
Sophia Huebler, Rachel Morris, Joseph Rusinko

A dichotomy law for certain classes of phylogenetic networks
Michael Fuchs, Mike Steel
https://arxiv.org/abs/2506.23223 https://arxiv…

A dichotomy law for certain classes of phylogenetic networks
Many classes of phylogenetic networks have been proposed in the literature. A feature of many of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within this class. This has implications for their biological applicability, since some species -- which are the leaves of an underlying evolutionary network -- may be missing (e.g., they may have become extinct, or there are no data available for them) or we may simp…

On Ward Numbers and Increasing Schr\"oder Trees
Elena L. Wang, Guoce Xin
https://arxiv.org/abs/2507.15654 https://arxiv.org/pdf/…

On Ward Numbers and Increasing Schröder Trees
The Ward numbers $W(n,k)$ combinatorially enumerate set partitions with block sizes $\geq 2$ and phylogenetic trees (total partition trees). We prove that $W(n,k)$ also counts \emph{increasing Schröder trees} by verifying they satisfy Ward's recurrence. We construct a direct type-preserving bijection between total partition trees and increasing Schröder trees, complementing known type-preserving bijections to set partitions (including Chen's decomposition for increasing Schröder trees). Weig…

phylo2vec: a library for vector-based phylogenetic tree manipulation
Neil Scheidwasser, Ayush Nag, Matthew J Penn, Anthony MV Jakob, Frederik M{\o}lkj{\ae}r Andersen, Mark P Khurana, Landung Setiawan, Madeline Gordon, David A Duch\^ene, Samir Bhatt
https://arxiv.org/abs/2506.19490

phylo2vec: a library for vector-based phylogenetic tree manipulation
Phylogenetics is a fundamental component of many analysis frameworks in biology as well as linguistics to study the evolutionary relationships of different entities. Recently, the advent of large-scale genomics and the SARS-CoV-2 pandemic has underscored the necessity for phylogenetic software to handle large datasets of genomes or phylogenetic trees. While significant efforts have focused on scaling optimisation algorithms, visualization, and lineage identification, an emerging body of researc…

Distinguishing Phylogenetic Level-2 Networks with Quartets and Inter-Taxon Quartet Distances
Niels Holtgrefe, Elizabeth S. Allman, Hector Ba\~nos, Leo van Iersel, Vincent Moulton, John A. Rhodes, Kristina Wicke
https://arxiv.org/abs/2507.17308

Distinguishing Phylogenetic Level-2 Networks with Quartets and Inter-Taxon Quartet Distances
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been limited to phylogenetic level-1 networks, which allow no interdependence between reticulate events. In this work, we establish the theoretical foundations for a statistically consistent inference method for a much broader class: semi-directed level-2 networks …

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference
Tianyu Xie, Yicong Mao, Cheng Zhang
https://arxiv.org/abs/2507.18380 https://

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference
Probabilistic modeling over the combinatorially large space of tree topologies remains a central challenge in phylogenetic inference. Previous approaches often necessitate pre-sampled tree topologies, limiting their modeling capability to a subset of the entire tree space. A recent advancement is ARTree, a deep autoregressive model that offers unrestricted distributions for tree topologies. However, its reliance on repetitive tree traversals and inefficient local message passing for computing t…

Order-Dependent Dissimilarity Measures on Phylogenetic Trees
Simone Linz, Katherine St. John, Charles Semple, Kristina Wicke
https://arxiv.org/abs/2507.11254 https://

Order-Dependent Dissimilarity Measures on Phylogenetic Trees
Ordered leaf attachment, Phylo2Vec, and HOP are three recently introduced vector representations for rooted phylogenetic trees where the representation is determined by an ordering of the underlying leaf set X. Comparing the vectors of two rooted phylogenetic X-trees T and T' for a fixed ordering on X leads to polynomial-time computable measure for the dissimilarity of T and T', albeit dependent on the choice of the leaf ordering. For each of ordered leaf attachment, Phylo2Vec, and HOP, we comp…

Replaced article(s) found for q-bio.PE. https://arxiv.org/list/q-bio.PE/new
[1/1]:
- Phylogenetic invariants: straightforward from the general Markov to equivariant models
Marta Casanellas, Jes\'us Fern\'andez-S\'anchez

Replaced article(s) found for q-bio.PE. https://arxiv.org/list/q-bio.PE/new
[1/1]:
- Metrics for classes of semi-binary phylogenetic networks using $\mu$-representations
Christopher Reichling, Leo van Iersel, Yukihiro Murakami

This https://arxiv.org/abs/1206.3472 has been replaced.
link: https://scholar.google.com/scholar?q=a

Perfect taxon sampling and fixing taxon traceability: Introducing a class of phylogenetically decisive collections of taxon sets
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees describing the phylogenetic relationships of the (input) species sets are compatible, they can only be combined into a common supertree in precisely one way. This setting is sometimes also referred to as \enquote{perfect taxon sampling}. While for rooted trees, the…

This https://arxiv.org/abs/1206.3472 has been replaced.
link: https://scholar.google.com/scholar?q=a

Perfect taxon sampling and fixing taxon traceability: Introducing a class of phylogenetically decisive collections of taxon sets
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees describing the phylogenetic relationships of the (input) species sets are compatible, they can only be combined into a common supertree in precisely one way. This setting is sometimes also referred to as \enquote{perfect taxon sampling}. While for rooted trees, the…

A strengthened bound on the number of states required to characterize maximum parsimony distance
Mareike Fischer, Steven Kelk, Sofia Vazquez Alferez
https://arxiv.org/abs/2506.09888

A strengthened bound on the number of states required to characterize maximum parsimony distance
In this article we prove that the distance $d_{\mathrm{MP}}(T_1,T_2) = k$ between two unrooted binary phylogenetic trees $T_1, T_2$ on the same set of taxa can be defined by a character that is convex on one of $T_1, T_2$ and which has at most $2k$ states. This significantly improves upon the previous bound of $7k-5$ states. We also show that for every $k \geq 1$ there exist two trees $T_1, T_2$ with $d_{\mathrm{MP}}(T_1,T_2) = k$ such that at least $k+1$ states are necessary in any character t…