scholarly journals Automated Testing of Unix Command-line and Scripting Skills

2006 ◽  
Author(s):  
Andrew Solomon ◽  
Daniel Santamaria ◽  
Raymond Lister
Keyword(s):  
Automated Testing ◽  
Command Line ◽  
Unix Command

scholarly journals Phylonium: fast estimation of evolutionary distances from large samples of similar genomes

2019 ◽  
Vol 36 (7) ◽  
pp. 2040-2046 ◽  
Author(s):  
Fabian Klötzl ◽  
Bernhard Haubold
Keyword(s):  
Disease Outbreaks ◽  
Supplementary Information ◽  
Whole Genome ◽  
Command Line ◽  
Supplementary Data ◽  
Large Samples ◽  
Fast Estimation ◽  
Unix Command ◽  
Similar Accuracy ◽  
Single Sequence

Abstract Motivation Tracking disease outbreaks by whole-genome sequencing leads to the collection of large samples of closely related sequences. Five years ago, we published a method to accurately compute all pairwise distances for such samples by indexing each sequence. Since indexing is slow, we now ask whether it is possible to achieve similar accuracy when indexing only a single sequence. Results We have implemented this idea in the program phylonium and show that it is as accurate as its predecessor and roughly 100 times faster when applied to all 2678 Escherichia coli genomes contained in ENSEMBL. One of the best published programs for rapidly computing pairwise distances, mash, analyzes the same dataset four times faster but, with default settings, it is less accurate than phylonium. Availability and implementation Phylonium runs under the UNIX command line; its C++ sources and documentation are available from github.com/evolbioinf/phylonium. Supplementary information Supplementary data are available at Bioinformatics online.

A Unix command line argument processor

2003 ◽  
Author(s):  
T.L. Crawford ◽  
R.O. Pettus
Keyword(s):  
Command Line ◽  
Unix Command

scholarly journals Galactic Circos: User-friendly Circos plots within the Galaxy platform

GigaScience ◽  
2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Helena Rasche ◽  
Saskia Hiltemann
Keyword(s):  
Analytical Data ◽  
Genomic Analysis ◽  
Scientific Data ◽  
Ease Of Use ◽  
Command Line ◽  
Web Browser ◽  
The Galaxy ◽  
Unix Command ◽  
User Friendly ◽  
High Degree

Abstract Background Circos is a popular, highly flexible software package for the circular visualization of complex datasets. While especially popular in the field of genomic analysis, Circos enables interactive graphing of any analytical data, including alternative scientific domain data and non-scientific data. This high degree of flexibility also comes with a high degree of complexity, which may present an obstacle for researchers not trained in programming or the UNIX command line. The Galaxy platform provides a user-friendly browser-based graphical interface incorporating a broad range of “wrapped” command line tools to facilitate accessibility. Findings We have developed a Galaxy wrapper for Circos, thus combining the power of Circos with the accessibility and ease of use of the Galaxy platform. The combination substantially simplifies the specification and configuration of Circos plots for end users while retaining the power to produce publication-quality visualizations of complex multidimensional datasets. Conclusions Galactic Circos enables the creation of publication-ready Circos plots using only a web browser, via the Galaxy platform. Users may download the full set of Circos configuration files of their plots for further manual customization. This version of Circos is available as an open-source installable application from the Galaxy ToolShed, with its use clarified in a training manual hosted by the Galaxy Training Network.

scholarly journals A guide to phylotranscriptomic analysis for phycologists

ALGAE ◽  
2021 ◽  
Vol 36 (4) ◽  
pp. 333-340
Author(s):  
Seongmin Cheon ◽  
Sung-Gwon Lee ◽  
Hyun-Hee Hong ◽  
Hyun-Gwan Lee ◽  
Kwang Young Kim ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Transcriptome Sequencing ◽  
Evolutionary Biology ◽  
Low Cost ◽  
Phylogenetic Analyses ◽  
Genomic Data ◽  
Command Line ◽  
Command Line Interface ◽  
Training And Education ◽  
Unix Command

Phylotranscriptomics is the study of phylogenetic relationships among taxa based on their DNA sequences derived from transcriptomes. Because of the relatively low cost of transcriptome sequencing compared with genome sequencing and the fact that phylotranscriptomics is almost as reliable as phylogenomics, the phylotranscriptomic analysis has recently emerged as the preferred method for studying evolutionary biology. However, it is challenging to perform transcriptomic and phylogenetic analyses together without programming expertise. This study presents a protocol for phylotranscriptomic analysis to aid marine biologists unfamiliar with UNIX command-line interface and bioinformatics tools. Here, we used transcriptomes to reconstruct a molecular phylogeny of dinoflagellate protists, a diverse and globally abundant group of marine plankton organisms whose large and complex genomic sequences have impeded conventional phylogenic analysis based on genomic data. We hope that our proposed protocol may serve as practical and helpful information for the training and education of novice phycologists.

The UNIX Command Line

2017 ◽  
pp. 1-21
Author(s):  
Bernhard Haubold ◽  
Angelika Börsch-Haubold
Keyword(s):  
Command Line ◽  
Unix Command
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