Software description - nselem/corason GitHub Wiki

CORASON was developed on Perl, uses blastp to find similar sequenceson a Bacteria database, muscle to align them and Gblocks to keep only informative regions.

Docker

[Docker] (https://www.docker.com/) is a software containerization platform that guarantees reproducibility. Docker containers wrap a piece of software in a complete filesystem that contains everything needed to run: code, runtime, system tools, system libraries – anything that can be installed on a server. This allows that the software will always run the same, regardless of its environment.
. Docker is an open platform for distribute applications created for developers and sysadmins. Among docker advantages are reproducibility and compatibility on practically every machine.

On CORASON docker has been used to construct a minimal linux where CORASON dependencies were properly installed, that way, end users doesn't have to deal with installation issues. The only installation will be Docker engine, but once installed there are many images constructed on the DockerHub that bioinformaticists may found useful.

Perl

[Perl] (https://www.perl.org/) is a programming language widely used in bioinformatics

CORASON output contains an SVG file, SVG stands for scalable vector graphics. SVG files are scalable, high quality figures, that never loose resolution. SVG images can be created and edited with any text editor. All major modern web browsers—including Mozilla Firefox, Internet Explorer, Google Chrome, Opera, Safari, and Microsoft Edge—have at least some degree of SVG rendering support.

Perl is a highly capable, feature-rich programming language with over 29 years of development widely used to develop bioinformatic tools.

• SVG perl module
  [perl SVG] (http://perlmaven.com/scalable-vector-graphics-with-perl) introduction at perl Maven
  [SVG ] http://www.w3schools.com/svg/ tutorial at W3 schools

BLAST

Blast finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

MUSCLE

[MUSCLE] (http://www.drive5.com/muscle/) stands for MUltiple Sequence Comparison by Log- Expectation. is a Sequence alignment tool,

Gblocks

[Gblocks] (http://molevol.cmima.csic.es/castresana/Gblocks.html)

Quicktree

[quicktree] (http://www.sanger.ac.uk/science/tools/quicktree)

Newick Utilities

• [newick tools] (http://cegg.unige.ch/newick_utils)

RAST

RAST Rapid annotation using subsystems technology.