scholarly journals SFS_CODE: More Efficient and Flexible Forward Simulations

2015 ◽  
Author(s):  
Ryan D. Hernandez ◽  
Lawrence H. Uricchio
Keyword(s):  
Human Genome ◽  
Open Source Software ◽  
General Public ◽  
Population Genetic ◽  
Genome Structure ◽  
Supplementary Information ◽  
Selective Sweeps ◽  
Complex Models ◽  
Soft Selective Sweeps ◽  
General Public License

SUMMARY: Modern implementations of forward population genetic simulations are efficient and flexible, enabling the exploration of complex models that may otherwise be intractable. Here we describe an updated version of SFS_CODE, which has increased efficiency and includes many novel features. Among these features is an arbitrary model of dominance, the ability to simulate partial and soft selective sweeps, as well as track the trajectories of mutations and/or ancestries across multiple populations under complex models that are not possible under a coalescent framework. We also release sfs_coder, a Python wrapper to SFS_CODE allowing the user to easily generate command lines for common models of demography, selection, and human genome structure, as well as parse and simulate phenotypes from SFS_CODE output. Availability and Implementation: Our open source software is written in C and Python, and are available under the GNU General Public License at http://sfscode.sourceforge.net. Contact: [email protected] Supplementary information: Detailed usage information is available from the project website at http://sfscode.sourceforge.net.

scholarly journals discoal: flexible coalescent simulations with selection

2016 ◽  
Author(s):  
Andrew D. Kern ◽  
Daniel R. Schrider
Keyword(s):  
Programming Language ◽  
Source Code ◽  
Recurrent Mutation ◽  
Supplementary Information ◽  
Selective Sweeps ◽  
C Programming Language ◽  
Coalescent Simulations ◽  
C Programming ◽  
Soft Selective Sweeps ◽  
General Public License

AbstractSummaryHere we describe discoal, a coalescent simulator able to generate population samples that include selective sweeps in a feature-rich, flexible manner. discoal can perform simulations conditioning on the fixation of an allele due to drift or either hard or soft selective sweeps—even those occurring a large genetic distance away from the simulated locus. discoal can simulate sweeps with recurrent mutation to the adaptive allele, recombination, and gene conversion, under nonequilibrium demographic histories and without specifying an allele frequency trajectory in advance.Availability and ImplementationAvailability and implementation: discoal is implemented in the C programming language. Source code is freely available on GitHub (https://github.com/kernlab/discoal_multipop) under a GNU General Public [email protected] informationSupplementary Figures and Text are appended below

scholarly journals A fast and memory-efficient implementation of the transfer bootstrap

2019 ◽  
Vol 36 (7) ◽  
pp. 2280-2281 ◽  
Author(s):  
Sarah Lutteropp ◽  
Alexey M Kozlov ◽  
Alexandros Stamatakis
Keyword(s):  
General Public ◽  
Efficient Implementation ◽  
Supplementary Information ◽  
Bootstrap Support ◽  
Supplementary Data ◽  
Original Algorithm ◽  
Parallel Version ◽  
Branch Support ◽  
General Public License ◽  
Memory Efficient

Abstract Motivation Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Results We developed a fast and memory-efficient TBE implementation. We improve upon the original algorithm by Lemoine et al. via several algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× to 40× memory savings compared with booster. Availability and implementation Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallel version that also computes additional TBE-related statistics is available at: https://github.com/lutteropp/raxml-ng/tree/tbe. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Soft selective sweeps in evolutionary rescue

2016 ◽  
Author(s):  
Benjamin A. Wilson ◽  
Pleuni S. Pennings ◽  
Dmitri A. Petrov
Keyword(s):  
Drug Resistance ◽  
Population Genetics ◽  
Population Genetic ◽  
Genetic Adaptation ◽  
Selective Sweeps ◽  
Adaptive Mutations ◽  
Evolutionary Rescue ◽  
Large Populations ◽  
Genetic Signatures ◽  
Soft Selective Sweeps

AbstractEvolutionary rescue occurs when a population that is declining in size because of an environmental change is rescued by genetic adaptation. Evolutionary rescue is an important phenomenon at the intersection of ecology and population genetics. While most population genetic models of evolutionary rescue focus on estimating the probability of rescue, we focus on whether one or more adaptive lineages contribute to evolutionary rescue. We find that when evolutionary rescue is likely, it is often driven by soft selective sweeps where multiple adaptive mutations spread through the population simultaneously. We give full analytic results for the probability of evolutionary rescue and the probability that evolutionary rescue occurs via soft selective sweeps in our model. We expect that these results will find utility in understanding the genetic signatures associated with various evolutionary rescue scenarios in large populations, such as the evolution of drug resistance in viral, bacterial, or eukaryotic pathogens.

scholarly journals FENOMENA LINUX, SUATU TEROBOSAN NETWORK ORGANIZATION DALAM ERA PEMASARAN RELASIONAL

2003 ◽  
Vol 2 (1) ◽  
Author(s):  
Dudi Anandya
Keyword(s):  
Operating System ◽  
Open Source ◽  
Open Source Software ◽  
General Public ◽  
Free Software ◽  
Network Organization ◽  
New Concepts ◽  
General Public License

Linux is an operating system that it's presence offer many "new concepts" to the market. It’s an open source software developed under GNU project using General Public License (GPL), that gives everyone freedom to run, copy, distribute, study, change, and improve the software. The GNU Project was launched in 1984 to develop a complete Unix-like operating system which is free software: the GNU system. GNU is a recursive acronym for "GNU's Not Unix”; it is pronounced “guh-NEW", In Other way we can say that Linux developed, manufactured, and distributed by it's own costumers. They joined together in the Linux communities and create a network among them. It has a unique lateral pattern of relationship. The Author named all of this as the “Linux Phenomenon". This articles will begin by explaining theories about network, and then discuss the and then discuss the Linux phenomenon. Later, the author will explore the Linux's "breakthrough" in networking, and the implication of "how to do business".

scholarly journals GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

2019 ◽  
Author(s):  
Pierre-Alain Chaumeil ◽  
Aaron J Mussig ◽  
Philip Hugenholtz ◽  
Donovan H Parks
Keyword(s):  
General Public ◽  
Source Code ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Computationally Efficient ◽  
Taxonomic Assignments ◽  
General Public License

Abstract Summary The GTDB Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the Genome Taxonomy Database (GTDB). GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel. Here we demonstrate the accuracy of the GTDB-Tk taxonomic assignments by evaluating its performance on a phylogenetically diverse set of 10,156 bacterial and archaeal metagenome-assembled genomes. Availability GTDB-Tk is implemented in Python and licensed under the GNU General Public License v3.0. Source code and documentation are available at: https://github.com/ecogenomics/gtdbtk Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals ARBitR: an overlap-aware genome assembly scaffolder for linked reads

2020 ◽  
Author(s):  
Markus Hiltunen ◽  
Martin Ryberg ◽  
Hanna Johannesson
Keyword(s):  
Genome Assembly ◽  
General Public ◽  
Source Code ◽  
Draft Genome ◽  
Supplementary Information ◽  
Genomic Sequencing ◽  
Supplementary Data ◽  
Genome Assemblies ◽  
General Public License

Abstract Summary Linked genomic sequencing reads contain information that can be used to join sequences together into scaffolds in draft genome assemblies. Existing software for this purpose performs the scaffolding by joining sequences with a gap between them, not considering potential overlaps of contigs. We developed ARBitR to create scaffolds where overlaps are taken into account and show that it can accurately recreate regions where draft assemblies are broken. Availability and implementation ARBitR is written and implemented in Python3 for Unix-based operative systems. All source code is available at https://github.com/markhilt/ARBitR under the GNU General Public License v3. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals IMPLEMENTASI GLPI (GESTIONNAIRE LIBRE DE PARC INFORMATIQUE) UNTUK LAYANAN IT, MANAJEMEN ASET DAN RESERVASI ASET

2020 ◽  
Author(s):  
Dwika Nur Ridlo Robby
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Asset Management ◽  
General Public ◽  
Management System ◽  
It Management ◽  
Management Software ◽  
Service Desk ◽  
General Public License

The purpose of this research is to implement IT asset management and tools using open source software. The software used is GLPI (Gestionnaire Libre de Parc Informatique), an Asset and IT management system package that provides the Service Desk, License Tracking and Software Audit features. GLPI is a free asset and IT management software, a software for asset management, with an additional interface for filing requests and also for reporting related to IT technicians who write in php language and are distributed under the GPL license (General Public License).

scholarly journals Next Generation HGVS Nomenclature Checker

2021 ◽  
Author(s):  
Mihai Lefter ◽  
Jonathan K Vis ◽  
Martijn Vermaat ◽  
Johan T den Dunnen ◽  
Peter E M Taschner ◽  
...  
Keyword(s):  
Open Source ◽  
Human Genome ◽  
General Public ◽  
Scientific Literature ◽  
Source Code ◽  
Genetic Diagnostics ◽  
Clinical Genetic ◽  
Human Genome Variation Society ◽  
Open Source Project ◽  
General Public License

ABSTRACT Motivation Unambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature, and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. Results Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in approximately 50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for approximately 7% of cases, Mutalyzer was able to automatically correct the description. Availability Mutalyzer is an Open Source project under the GNU Affero General Public License. The source code is available on GitHub (https://github.com/mutalyzer/mutalyzer) and a running instance is available at: https://mutalyzer.nl.

scholarly journals ARBitR: An overlap-aware genome assembly scaffolder for linked reads

2020 ◽  
Author(s):  
Markus Hiltunen ◽  
Martin Ryberg ◽  
Hanna Johannesson
Keyword(s):  
Genome Assembly ◽  
General Public ◽  
Source Code ◽  
Draft Genome ◽  
Supplementary Information ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Long Read ◽  
Genome Assemblies ◽  
General Public License

Abstract10X Genomics Chromium linked reads contain information that can be used to link sequences together into scaffolds in draft genome assemblies. Existing software for this purpose perform the scaffolding by joining sequences together with a gap between them, not considering potential contig overlaps. Such overlaps can be particularly prominent in genome drafts assembled from long-read sequencing data where an overlap-layout-consensus (OLC) algorithm has been used. Ignoring overlapping contig ends may result in genes and other features being incomplete or fragmented in the resulting scaffolds. We developed the application ARBitR to generate scaffolds from genome drafts using 10X Chromium data, with a focus on minimizing the number of gaps in resulting scaffolds by incorporating an OLC step to resolve junctions between linked contigs. We tested the performance of ARBitR on three published and simulated datasets and compared to the previously published tools ARCS and ARKS. The results revealed that ARBitR performed similarly considering contiguity statistics, and the advantage of the overlapping step was revealed by fewer long and short variants in ARBitR produced scaffolds, in addition to a higher proportion of completely assembled LTR retrotransposons. We expect ARBitR to have broad applicability in genome assembly projects that utilize 10X Chromium linked reads.Availability and implementationARBitR is written and implemented in Python3 for Unix-like operative systems. All source code is available at https://github.com/markhilt/ARBitR under the GNU General Public License [email protected] informationavailable online

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