Search Results for "horizontal gene transfer"
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Showing 9 open source projects for "horizontal gene transfer"
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LibreNMS
Community-based GPL-licensed network monitoring system
Welcome to LibreNMS, a fully featured network monitoring system that provides a wealth of features and device support. LibreNMS is an auto-discovering PHP/MySQL/SNMP-based network monitoring that includes support for a wide range of network hardware and operating systems including Cisco, Linux, FreeBSD, Juniper, Brocade, Foundry, HP, and many more. -
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Flexe
The open source federated learning for vehicular network simulation
Flexe is a FL simulator designed for connected and autonomous vehicles (CAVs). It enables horizontal/vertical/transfer FL schemes and simulates realistic wireless and vehicular dynamics. Separate Python client (PyFlexe) available. -
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scArches
Reference mapping for single-cell genomics
Single-cell architecture surgery (scArches) is a package for reference-based analysis of single-cell data. scArches allows your single-cell query data to be analyzed by integrating it into a reference atlas. By mapping your data into an integrated reference you can transfer cell-type annotation from reference to query, identify disease states by mapping to healthy atlas, and advanced applications such as imputing missing data modalities or spatial locations. -
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
Raw genomic sequences are frequently contaminated with sequences of other organism. Their identification is essential for the interpretation of genomic data. In this context it is essential to distinguish between horizontal gene transfers and contamination. The genomic context of sequences can help distinguish the two scenarios. Taxoblast splits genomic scaffolds into sub-sequences of defined length and for each of them determines the closest related taxon. It then summarizes this information for the entire scaffold, taking into account the taxonomic ontology. ... -
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AccNET
AccNET: Accessory Genome Constellation Network.
...AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical structures. AccNET has moved to GitHub Repository: https://github.com/valflanza/accnet -
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LGTmate
Lateral Gene Transfer utility
LGTmate is a simple and powerful bioinformatic software tool to identify lateral gene transfer events and contaminants in Eukaryotic proteomes. It is available as a GUI or command-line application, with no dependencies and no installation required. -
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WODA solver
A finite volume groundwater simulator
WODA (Well Outline and Design Aid) is a groundwater simulator developed at the Group for Numerical Analysis, Jaroslav Cerni Institute, Belgrade, Serbia. WODA does not have its own graphical user interface, but it can work with groundwater models constructed using the freely available Lizza interface, http://www.bioirc.ac.rs/index.php/groundwater-flow-software. -
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Protospacer
Rapid gRNA design and validation for CRISPR
...Protospacer allows researchers to build, analyze, and share their own database of CRISPR target-sites. This enables the development of custom libraries and helps to transfer the CRISPR technology to new organisms. Each Protospacer database is a simple catalogue of all possible Cas9 target-sites within a given FASTA sequence, i.e. all NGG/NAG sites. Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. ... -
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LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.
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