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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Mapping the intrinsic photocurrent streamlines through micromagnetic heterostructure devices

Photocurrent in quantum materials is often collected at global contacts far away from the initial photoexcitation. This collection process is highly nonlocal. It involves an intricate spatial pattern of photocurrent flow (streamlines) away from its primary photoexcitation that depends sensitively on the configuration of current collecting contacts as well as the spatial nonuniformity and tensor structure of conductivity. Direct imaging to track photocurrent streamlines is challenging. Here, we demonstrate a microscopy method to image photocurrent streamlines through ultrathin heterostructure devices comprising platinum on yttrium iron garnet (YIG). We accomplish this by combining scanning photovoltage microscopy with a uniform rotating magnetic field. Here, local photocurrent is generated through a photo-Nernst type effect with its direction controlled by the external magnetic field. This enables the mapping of photocurrent streamlines in a variety of geometries that include conventional Hall bar-type devices, but also unconventional wing-shaped devices called electrofoils. In these, we find that photocurrent streamlines display contortion, compression, and expansion behavior depending on the shape and angle of attack of the electrofoil devices, much in the same way as tracers in a wind tunnel map the flow of air around an aerodynamic airfoil. This affords a powerful tool to visualize and characterize charge flow in optoelectronic devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Democratizing life cycle assessment by developing a streamlined model of greenhouse gas emissions from US natural gas supply chains

Natural gas (NG) supply chains contribute substantially to the global energy supply and anthropogenic methane emissions, making them frequent subjects of life cycle assessments (LCAs). To better characterize central tendencies and variability, we systematically reviewed and harmonized published estimates of life cycle greenhouse gas (GHG) emissions from United States NG supply chains. Results informed a streamlined LCA model (SLiNG-GHG: streamlined LCAs of NG-GHGs) that quantifies carbon dioxide and methane from three gates: transmission, distribution, and shipping. Median estimates employing harmonized emission inputs, are 10, 11, and 21 g CO2e/MJ gas (100-year global warming potentials [GWPs]), and 20, 22, and 33 g CO2e/MJ gas (20-year GWPs), delivered to each gate, respectively. Alternatively, inputting available, independent methane measurements, SLiNG-GHG estimates varied from -23% to +316% relative to baseline. Bottom-up inventories used in LCAs tend to underestimate methane compared with measurements. Results underscore the need for open-source, streamlined LCA models that can easily incorporate rapidly evolving measurements for non-experts like investors and regulators.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2024

PNNL Review of Federal and State Agency Regulatory Streamlining Practices

All major federal actions that have the potential to significantly affect the environment (e.g., land purchases and/or issuing grants, permits, leases, or licenses) are subject to multiple statutes including the following: • an environmental analysis under the National Environmental Policy Act (NEPA) • potential consultations with the U.S. Fish and Wildlife Service (USFWS) and/or National Marine Fisheries Service (NMFS) under the Endangered Species Act of 1973, as amended (ESA) • potential consultations with State Historical Preservation Officers (SHPOs) and/or tribal nations [often Tribal Historic Preservation Officers (THPOs)] under the National Historic Preservation Act of 1966 (NHPA). Given the size of the federal government and the corresponding variability and complexity in its missions, different branches within the federal government have a fairly wide range of approaches to fulfill their NEPA and consultation requitements. Many of these approaches are founded on the desire to streamline their NEPA and consultation processes while meeting the spirit and letter of the regulations. Some federal and state environmental/engineering agencies have developed web-based dashboards that provide a single web location for permit application submittals. They also use general permits in their various permitting processes. General permits can streamline the permitting process by establishing identical requirements for all eligible applicants. This reduces the time these agencies need to spend reviewing individual permits and setting specific requirements. In addition, general permits do not require a case-specific permit application. This paper presents a sampling of effective agency examples of streamlining the NEPA process and associated agency consultations. It also includes several examples of federal and state agency web portals, online application systems, and general permits that make application processes more efficient and accessible.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Implementation of a High-Mach Integral Boundary Layer Method for Arbitrary Streamlined Body Geometry

The Momentum-Energy Integral Technique (MEIT) is an integral boundary layer method for the high-Mach flow regime used to approximate heat transfer and viscous force quantities of interest along streamlines of an inviscid flow solution on the surface of a flight vehicle. This method allows rapid mid-fidelity estimation of these quantities which would otherwise require a much more expensive viscous flow solution to produce. Integral boundary layer methods like MEIT have been around for decades, though usually only formulated for simple geometries such as 2-dimensional wing shapes or axi-symmetric nose shapes. The implementation discussed herein has been generalized to apply to any 3-dimensional streamlined body geometry through correct treatment of the curvilinear axes (streamline attached) momentum and energy entrainment terms, and handling of arbitrary stagnation region geometry. This implementation is provided as a software package for the Python environment, along with readers for common inviscid flow solution providers such as NASA’s CART3D flow solver.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ (R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. Furthermore, this result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides, providing a streamlined method for addressing genetic engineering challenges in the yeast.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Streamlined Loads Analysis of Floating Wind Turbines With Fiber Rope Mooring Lines

This paper presents an approach for more accurate yet relatively streamlined accounting for the nonlinear characteristics of synthetic fiber rope mooring lines for floating wind turbines. First, we select a minimal set of parameters that can efficiently approximate a mooring line material's quasi-static and dynamic stiffness characteristics. We also develop a set of baseline coefficients for different rope materials based on published product information and research papers. We then expand a quasi-static mooring model to include dynamic mooring line stiffness terms in a way that allows the nonlinear stiffness behavior of fiber ropes to be considered even in quasi-static analyses. For dynamic analysis, we have updated the model MoorDyn, coupled with OpenFAST, to work with the new dynamic mooring line stiffness terms. This includes the implementation of a new viscoelastic approach that allows the tension-strain relation of each mooring line segment to vary between two stiffness values, depending on the strain rate. After presenting the formulation of the approaches for modeling synthetic ropes, they are demonstrated on a floating wind turbine mooring system with taut polyester rope mooring lines. The results are compared with those of other approaches of similar fidelity, including the static-dynamic method and separate simulations with static and dynamic stiffness values. Comparing the results shows the ability of the new method to match the results of the previous methods in a more streamlined manner.

elasticity↗
DOE OSTI2025

Data for "RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides"

For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ ( R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. This result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides , providing a streamlined method for addressing genetic engineering challenges in the yeast.

gene editing↗
DOE OSTI2026

Generalized Integral Boundary Layer Equations in Streamline Curvilinear Coordinates

The MEIT equations are derived in orthogonal streamline curvilinear coordinates defined by the inviscid velocity at the wall and the surface-normal direction. The resulting formulations is (1) is not restricted to flat-plate or axisymmetric geometries, (2) accommodates vortical inviscid flows (e.g., induced by curved shocks) and wall mass blowing, and (3) allows for an arbitrary definition of the edge state. The streamline ODEs are also extended to a surface PDE framework.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Streamlined Loads Analysis of Floating Wind Turbines With Fiber Rope Mooring Lines: Preprint

This paper presents an approach for more accurate yet relatively streamlined accounting for the nonlinear characteristics of synthetic fiber rope mooring lines for floating wind turbines. First, we select a minimal set of parameters that can efficiently approximate a mooring line material's quasi-static and dynamic stiffness characteristics. We also develop a set of baseline coefficients for different rope materials based on published product information and research papers. We then expand a quasi-static mooring model to include dynamic mooring line stiffness terms in a way that allows the nonlinear stiffness behavior of fiber ropes to be considered even in quasi-static analyses. For dynamic analysis, we have updated the model MoorDyn, coupled with OpenFAST, to work with the new dynamic mooring line stiffness terms. This includes the implementation of a new viscoelastic approach that allows the tension-strain relation of each mooring line segment to vary between two stiffness values depending on the strain rate. After presenting the formulation of the approaches for modeling synthetic ropes, they are demonstrated on a floating wind turbine mooring system with taut polyester rope mooring lines. The results are compared with those of other approaches of similar fidelity including the static-dynamic method and separate simulations with static and dynamic stiffness values. Comparing the results shows the ability of the new method to match the results of the previous methods in a more streamlined manner.

elasticity↗
DOE OSTI2021

Streamlined Approach for Environmental Restoration (SAFER) Plan for Corrective Action Unit 572: Test Cell C Ancillary Building and Structures - Nevada National Security Site, Nevada with ROTC 1

This Streamlined Approach for Environmental Restoration (SAFER) Plan addresses the actions needed to achieve closure for Corrective Action Unit (CAU) 572, Test Cell C Ancillary Building and Structures, identified in the Federal Facility Agreement and Consent Order (FFACO). CAU 572 comprises the following corrective action sites (CASs) located in Area 25 of the Nevada National Security Site: CAS 25-33-01, Building 3220, Equipment Building; CAS 25-33-02, Building 3230, Motor Drive Building; CAS 25-33-03, Building 3231, Pump House; CAS 25-33-04, Building 3232, Cryogenic Evaluation Lab; CAS 25-99-22, Ancillary Facilities. This plan provides the methodology for field activities needed to gather the necessary information for closing CAU 572. There is sufficient information and process knowledge from historical documentation and investigations of similar sites regarding the expected nature and extent of potential contaminants to recommend closure of CAU 572 using the SAFER process. Additional information will be obtained by conducting a field investigation before selecting the appropriate corrective action. It is anticipated that the results of the field investigation and implementation of corrective actions will support a defensible recommendation that no further corrective action is necessary. The purpose of the corrective action investigation (CAI) will be to document and verify the adequacy of existing information; to affirm the decision for either clean closure, closure in place, or no further action; and to provide sufficient data to implement the corrective action. The actual corrective action selected will be based on characterization activities implemented under this SAFER Plan. If it is determined that complete clean closure cannot be accomplished during the CAI, then a hold point will have been reached and the Nevada Division of Environmental Protection (NDEP) will be consulted to determine whether the remaining contamination will be closed under the alternative corrective action of closure in place. This will be presented in a closure report that will be prepared and submitted to NDEP for review and approval.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Streamlined Approach for Environmental Restoration (SAFER) Plan for Corrective Action Unit 114: Area 25 EMAD Facility Nevada National Security Site, Nevada

This Streamlined Approach for Environmental Restoration (SAFER) Plan addresses the actions needed to achieve closure for Corrective Action Unit (CAU) 114, Area 25 EMAD Facility, identified in the Federal Facility Agreement and Consent Order (FFACO). CAU 114 comprises the following corrective action sites (CASs) located in Area 25 of the Nevada National Security Site: • 25-41-03, EMAD Facility (Building 3900) • 25-99-23, Manned Control Car (MCC) and Engine Installation Vehicle (EIV) • 25-33-05, Building 3901, Engine Transport System Maintenance Building (Train Shed) This plan provides the methodology for field activities needed to gather the necessary information for closing CAU 114. There is sufficient information and process knowledge from historical documentation and investigations of similar sites regarding the expected nature and extent of potential contaminants to recommend closure of CAU 114 using the SAFER process. Additional information will be obtained by conducting a field investigation before selecting the appropriate corrective actions for CAU 114. It is anticipated that the results of the field investigation and implementation of corrective actions will support a defensible recommendation that no further corrective action is necessary. The purpose of the corrective action investigation will be to document and verify the adequacy of existing information; to affirm the decision for either clean closure, closure in place, or no further action; and to provide sufficient data to implement the corrective action. The actual corrective action selected will be based on characterization activities implemented under this SAFER Plan. If specific conditions or findings fall outside the bounds of the conceptual site model, such as an unanticipated release, the Nevada Division of Environmental Protection (NDEP) will be consulted to determine the path forward before proceeding. Upon completion of SAFER activities, a closure report (CR) will be prepared and submitted to NDEP for review and approval. The schedule for completion of the CR will be established in consultation with NDEP.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Natural transformation as a tool in Acinetobacter baylyi : Streamlined engineering and mutational analysis

Natural transformation and homologous recombination in a soil bacterium, Acinetobacter baylyi ADP1, occur with exceptionally high efficiency. These genetic features can be harnessed to address a wide variety of fundamental and applied scientific topics. Recent advances in synthetic biology and laboratory evolution have led to renewed appreciation for the use of A. baylyi as a model organism. To complement several review articles that highlight new tool sets, this chapter focuses on simple protocols and examples of transformation assays that facilitate genetic analysis and engineering. Whole genome sequencing often reveals extensive genetic variation among closely related isolates that can confound the association of genotypic and phenotypic changes. In A. baylyi, such associations can be deciphered in unique ways by directly transforming cells with linear DNA fragments. The resulting allelic replacement, which occurs at high frequency, rapidly generates desired mutants via targeted chromosomal editing. Diverse screening and selection methods can be used to test hypotheses and streamline experimental strategies to reveal the significance of specific DNA sequences. Moreover, large procedural variations are well tolerated, and techniques can be readily adapted for new purposes. Furthermore, one goal of highlighting natural transformation methodology in A. baylyi is to expand the community of researchers using this versatile bacterial host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A streamlined approach to characterize microalgae strains for biomass productivity under dynamic climate simulation conditions

Screening microalgae strains under static light and temperature flask conditions cannot directly quantify the biomass productivities of algae growing in the dynamically fluctuating light and temperature conditions of outdoor ponds. In this effort, we describe a testing pipeline that screens for productivity under climate simulated conditions. A validated, miniaturized Laboratory Environmental Algae Pond Simulator (mini-LEAPS) photobioreactor was used to determine optimal medium salinities and biomass productivities of cold-tolerant microalgae collected from Arctic, subarctic, Antarctic, and subalpine habitats. Strains characterized in this effort include: Chlorella antarctica UTEX1959, Chlorella sp. UTEXSNO69, Chloromonas rosae UTEXSNO11, Phaeodactylum tricornutum UTEX646, and Stichococcus minutus CCALA727. Observed productivities of the characterized strains ranged from 1.74 ± 0.25 to 8.18 ± 0.81 g m –2 day –1 (as ash-free dry weight). For each strain, a temperature tolerance profile was generated to identify the most appropriate season (s) for cultivation. The two most promising strains, Chlorella sp. UTEX SNO69 and P. tricornutum UTEX646, were tested alongside the DISCOVR winter benchmark strain Monoraphidium minutum 26B-AM in outdoor open ponds at the PNNL Algae Testbed (PAT) in Arizona. Further, under cold-season outdoor pond conditions, Chlorella sp. UTEXSNO69 achieved average areal biomass productivities of 8.21 ± 0.50 g m –2 day –1 , not significantly different from that of the benchmark strain (8.52 ± 0.43 g m –2 day –1 , p > 0.05). Under spring outdoor pond conditions, P. tricornutum UTEX646 achieved average areal biomass productivities 10.34 ± 0.27 g m –2 day –1 , not significantly different from that of the benchmark (10.07 ± 0.50 g m –2 day –1 ) under the tested conditions (p > 0.05). The streamlined pipeline was thus demonstrated to successfully characterize productive microalgae strains for outdoor deployment by weeding out algae strains that were not productive under the tested dynamic light and temperature conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
DOE OSTI2024

A streamline coordinate analysis of a turbulent boundary layer subject to pressure gradients and curvature on the windward side of a bump

Direct numerical simulation (DNS) of a turbulent boundary layer over the Gaussian (Boeing) bump is performed. This boundary layer exhibits a series of adverse and favourable pressure gradients and convex and concave curvature effects before separating. These effects on turbulent boundary layers are characterised and compared with a lower-Reynolds-number flow over the same geometry. The momentum budgets are analysed in the streamline-aligned coordinate system upstream of the separation region. These momentum budgets allow the simplification of equations to facilitate an integral analysis. Integral-analysis-based approximations for Reynolds stresses in the inner and outer regions of the boundary layer are also formulated. The shear and wall-normal Reynolds stress profiles normalised by these approximations exhibit a better collapse compared with friction velocity and Zagarola–Smits normalisations in the strong favourable pressure gradient region and in the mild adverse pressure region that precedes it in this flow. Simplification of these Reynolds stress approximations along with results from the DNS are used to obtain semi-empirical approximations that are able to provide stress closure in terms of wall solution fields for the turbulent boundary layer under consideration.

42 ENGINEERING↗
DOE OSTI2020

Chespa: Streamlining Expansive Chemical Space Evaluation of Molecular Sets

Thousands of chemical properties can be calculated for small molecules, which can be used to place the molecules within the context of a broader “chemical space.” These definitions vary based on compounds of interest and the goals for the given chemical space definition. Here, we introduce a customizable (i.e., modular) Python module, chespa, built to easily assess different chemical space definitions through cluster-ing of compounds in these spaces and visualize trends of these clusters. To demonstrate this, chespa currently streamlines prediction of vari-ous molecule descriptors (predicted chemical properties, molecular substructures, AI-based chemical space, and chemical class ontology) in order to test 6 different chemical space definitions. Furthermore, we investigated how these varying definitions trend with mass spectrometry (MS)-based observability, i.e., the ability of a molecule to be observed with MS (e.g., as a function of the molecule ionizability), using an example data set from the U.S. EPA's Non-Targeted Analysis Collaborative Trial (ENTACT), where blinded samples had been analyzed previously, providing 1,398 data points. Improved understanding of observability would offer many advantages in small molecule identifica-tion, such as (i) a priori selection of experimental conditions based on suspected sample composition, (ii) the ability to reduce the number of candidate structures during compound identification by removing those less likely to ionize, and, in turn, (iii) a reduced false discovery rate and increased confidence in identifications. Factors controlling observability are not fully understood, making prediction of this property non-trivial and a prime candidate for chemical space analysis. Chespa is available at github.com/pnnl/chespa.

Nunez, Jamie↗
DOE OSTI2023

A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics

Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We develop a tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3000 (>9500) phosphopeptides from 1 (10) µg of cell lysate using the label-free method without a spectral library. It also enables precise quantification of ~600 phosphopeptides from 100 sorted cells (single-cell level input for the enriched phosphopeptides) and ~700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 µm (equivalent to ~100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales

Abstract There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

59 BASIC BIOLOGICAL SCIENCES↗