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1. dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra

   https://doi.org/10.1101/2023.06.15.545182  

   Huang, Xin ; Struck, Travis J ; Davey, Sean W ; Gutenkunst, Ryan N ( June 2023 , bioRxiv)

   dadi is a popular software package for inferring models of demographic history and natural selection from population genomic data. But using dadi requires Python scripting and manual parallelization of optimization jobs. We developed dadi-cli to simplify dadi usage and also enable straighforward distributed computing.

   dadi-cli is implemented in Python and released under the Apache License 2.0. The source code is available athttps://github.com/xin-huang/dadi-cli. dadi-cli can be installed via PyPI and conda, and is also available through Cacao on Jetstream2https://cacao.jetstream-cloud.org/.

    

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2. Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space

   https://doi.org/10.1186/s12859-024-05997-y  

   Sukumaran, Jeet ; Meila, Marina ( December 2024 , BMC Bioinformatics)

   Existing software for comparison of species delimitation models do not provide a (true) metric or distance functions between species delimitation models, nor a way to compare these models in terms of relative clustering differences along a lattice of partitions.

   is a Python package for analyzing and visualizing species delimitation models in an information theoretic framework that, in addition to classic measures of information such as the entropy and mutual information [1], provides for the calculation of the Variation of Information (VI) criterion [2], a true metric or distance function for species delimitation models that is aligned with the lattice of partitions.

   is available under the MIT license from its public repository (https://github.com/jeetsukumaran/piikun), and can be installed locally using the Python package manager ‘pip‘.

    

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3. CorDiffViz: an R package for visualizing multi-omics differential correlation networks

   https://doi.org/10.1186/s12859-021-04383-2  

   Yu, Shiqing ; Drton, Mathias ; Promislow, Daniel_E_L ; Shojaie, Ali ( October 2021 , BMC Bioinformatics)

   Differential correlation networks are increasingly used to delineate changes in interactions among biomolecules. They characterize differences between omics networks under two different conditions, and can be used to delineate mechanisms of disease initiation and progression.

   We present a new R package, , that facilitates the estimation and visualization of differential correlation networks using multiple correlation measures and inference methods. The software is implemented in , and , and is available athttps://github.com/sqyu/CorDiffViz. Visualization has been tested for the Chrome and Firefox web browsers. A demo is available athttps://diffcornet.github.io/CorDiffViz/demo.html.

   Our software offers considerable flexibility by allowing the user to interact with the visualization and choose from different estimation methods and visualizations. It also allows the user to easily toggle between correlation networks for samples under one condition and differential correlations between samples under two conditions. Moreover, the software facilitates integrative analysis of cross-correlation networks between two omics data sets.

    

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4. Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments

   https://doi.org/10.1099/ijsem.0.004698  

   Baesman, Shaun M ; Sutton, John M ; Fierst, Janna L ; Akob, Denise M ; Oremland, Ronald S ( June 2019 , International Journal of Systematic and Evolutionary Microbiology)

   A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93^T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93^Twas capable of acetylenotrophic and diazotrophic growth, grew at 22–37 °C, pH 6.3–8.5 and in the presence of 10–45 g l⁻¹NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93^Trepresented a member of the genusSyntrophotaleawith highest 16S rRNA gene sequence similarities toSyntrophotalea acetylenicaDSM 3246^T(96.6 %),Syntrophotalea carbinolicaDSM 2380^T(96.5 %), andSyntrophotalea venetianaDSM 2394^T(96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93^Thad low genome-wide average nucleotide identity (81–87.5 %) and <70 % digital DNA–DNA hybridization value with other members of the genusSyntrophotalea. The phylogenetic position of SFB93^Twithin the familySyntrophotaleaceaeand as a novel member of the genusSyntrophotaleawas confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species,Syntrophotalea acetylenivoranssp. nov., is proposed, with SFB93^T(=DSM 106009^T=JCM 33327^T=ATCC TSD-118^T) as the type strain.

    

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5. Vibrio floridensis sp. nov., a novel species closely related to the human pathogen Vibrio vulnificus isolated from a cyanobacterial bloom

   https://doi.org/10.1099/ijsem.0.005675  

   Grant, Trudy-Ann ; Jayakumar, Jane M. ; López-Pérez, Mario ; Almagro-Moreno, Salvador ( February 2023 , International Journal of Systematic and Evolutionary Microbiology)

   A Gram-stain-negative, rod-shaped bacterial strain, designatedVibrio floridensisIRLE0018 (=NRRL B-65642=NCTC 14661), was isolated from a cyanobacterial bloom along the Indian River Lagoon (IRL), a large and highly biodiverse estuary in eastern Florida (USA). The results of phylogenetic, biochemical, and phenotypic analyses indicate that this isolate is distinct from species of the genusVibriowith validly published names and is the closest relative to the emergent human pathogen,Vibrio vulnificus. Here, we present the complete genome sequence ofV. floridensisstrain IRLE0018 (4 535 135 bp). On the basis of the established average nucleotide identity (ANI) values for the determination of different species (ANI <95 %), strain IRLE0018, with an ANI of approximately 92 % compared with its closest relative,V. vulnificus, represents a novel species within the genusVibrio. To our knowledge, this represents the first time this species has been described. The results of genomic analyses ofV. floridensisIRLE0018 indicate the presence of antibiotic resistance genes and several known virulence factors, however, its pathogenicity profile (e.g. survival in serum, phagocytosis avoidance) reveals limited virulence potential of this species in contrast toV. vulnificus.

    

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