Hyper Recent

Phylogenetic trees and networks play a central role in biology, bioinformatics, and mathematical biology, and producing clear, informative visualizations of them is an important task. We present new algorithms for visualizing rooted phylogenetic networks as either combining or transfer networks, in both cladogram and phylogram style. In addition, we introduce a layout algorithm that aims to improve clarity by minimizing the total stretch of reticulate edges. To address the common issue that biological publications often omit machine-readable representations of depicted trees and networks, we also provide an image-based algorithm for extracting their topology from figures. All algorithms are implemented in our new PhyloSketch app, which is open source and freely available at: https://github.com/husonlab/phylosketch2.

Sketch, capture and layout phylogenies

Similar Papers

Similar Papers

biorxiv
Thu Apr 03 2025
TarDis: Achieving Robust and Structured Disentanglement of Multiple Covariates
Addressing challenges in domain invariance within single-cell genomics necessitates innovative strategies to manage the heterogeneity of multi-source datasets while maintaining the integrity of biological signals. We introduce TarDis, a novel deep generative model designed to disentangle intricate covariate structures across diverse biological datasets, distinguishing technical artifacts from true...
Inecik, K.
•
Kara, A.
•
Rose, A.
•
Haniffa, M.
•
Theis, F. J.

biorxiv
Thu Apr 03 2025
Improving Protein Interaction Prediction in GenPPi: A Novel Interaction Sampling Approach Preserving Network Topology
Computational prediction of protein-protein interactions (PPIs) is crucial for understanding cell biology and drug development, offering a promising alternative to costly and time-consuming experimental methods. While the original GenPPi software represented an advance in ab initio PPI network prediction from bacterial genomes, its reliance on high sequence similarity limited it. In this work, we ...
William, A.
•
Godoy, I.
•
Marquez, C.
•
Silva, L.
...•
Santos, A. R. d.

biorxiv
Thu Apr 03 2025
Differential T cell receptor gene expression analysis using the Wilcoxon test with similarity-based weighting
To better understand immune responses, comparing the abundance of T cell receptors (TCRs) between conditions can provide insights into which T cells have proliferated or were involved in immune activation. This requires methods that can accurately identify significant differences in TCR-seq data. For conventional RNA-seq data, well-established differential gene expression (DGE) analysis tools such...
Buytenhuijs, F.
•
Ankan, A.
•
Textor, J.

biorxiv
Thu Apr 03 2025
Evidence of off-target probe binding in the 10x Genomics Xenium v1 Human Breast Gene Expression Panel compromises accuracy of spatial transcriptomic profiling
The accuracy of spatial gene expression profiles generated by probe-based in situ spatially-resolved transcriptomic technologies depends on the specificity with which probes bind to their intended target gene. Off-target binding, defined as a probe binding to something other than the target gene, can distort a gene\'s true expression profile, making probe specificity essential for reliable transcr...
Hallinan, C.
•
Ji, H. J.
•
Salzberg, S. L.
•
Fan, J.

biorxiv
Thu Apr 03 2025
Natural language processing of gene descriptions for overrepresentation analysis with GeneTEA
Overrepresentation analysis (ORA) is used to identify the biological relationships in a list of genes by testing gene sets for enrichment in the query. However, the inconsistent definition and highly overlapping nature of gene set databases can make interpreting ORA results difficult. Here, we introduce GeneTEA, a model that takes in free-text gene descriptions and incorporates several natural lan...
Boyle, I. A.
•
Aquib, N. A.
•
Kocak, M.
•
Creasi, R.
...•
Dempster, J. M.

biorxiv
Thu Apr 03 2025
Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra
A fundamental challenge in mass spectrometry-based proteomics is determining which peptide generated a given MS2 spectrum. Peptide sequencing typically relies on matching spectra against a known sequence database, which in some applications is not available. Deep learning- based de novo sequencing can address this limitation by directly predicting peptide sequences from MS2 data. We have seen the ...
Lapin, J.
•
Nilsson, A.
•
Wilhelm, M.
•
Käll, L.

biorxiv
Thu Apr 03 2025
BioPKS Pipeline: An integrated platform for merging the computational design of chimeric type I polyketide synthases with enzymatic pathways for chemical biosynthesis
Synthetic biology offers the promise of manufacturing chemicals more sustainably than petrochemistry. Yet, both the rate at which biomanufacturing can synthesize these molecules and the net chemical accessible space are limited by existing pathway discovery methods which can often rely on arduous literature searches. Here, we present an automated retrobiosynthesis tool, BioPKS Pipeline, that simul...
Chainani, Y.
•
Diaz, J.
•
Guilarte-Silva, M.
•
Blay, V.
...•
Backman, T. W. H.

biorxiv
Thu Apr 03 2025
LncMamba: A Deep Learning Model for lncRNA Localization Prediction Based on the Mamba Model
Accurate prediction of long non-coding RNA (lncRNA) subcellular localization is crucial for understanding its biological functions. In this study, we propose a novel deep learning framework, LncMamba, which utilizes a two-layer FPN network for multi-scale feature extraction and introduces the Mamba network to lncRNA localization prediction tasks for the first time. Based on this, we improved the l...
Huang, B.
•
Luo, Y.
•
Zhuang, Y.
•
He, S.
•
Yuan, C.

biorxiv
Thu Apr 03 2025
TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization
High-throughput chromosome conformation capture sequencing (Hi-C) is a key technology for studying the three-dimensional (3D) structure of genomes and chromatin folding. Hi-C data reveals important patterns of genome organization such as topologically associating domains (TADs) and chromatin loops with critical roles in transcriptional regulation and disease etiology and progression. However, the ...
Li, C.
•
Mowlaei, M. E.
•
Human Genome Structural Variation Consortium,
•
HGSVC Functional Analysis Working Group,
...•
Shi, X.