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mjsull edited this page Sep 4, 2015 · 2 revisions

Above is the window available upon immediately opening Easyfig. Versions may vary slightly as the graphical user interface uses a style native to the operating system in use.

Annotation Files: A list of GenBank, EMBL, FASTA or multiFASTA files you wish to create a figure from.

Blast Files: A list of BLAST files for drawing the comparison between two annotation files. The annotation file above must be the query, and the annotation file below must be the reference. Valid input files are legacy blast and blast+ tab delimited output without headers and crunch files. Files must be made using BLASTn or tBLASTx. These are made using the -outfmt 6 tag in blast+ or –m 8 tag in legacy blast.

Generate blastn/tblastx Files: Will generate BLASTn or tBLASTx comparisons between loaded annotation files. Requires BLAST to be installed, see above for installation instructions.

IMPORTANT: tBLASTx is very memory expensive and it may not be possible to perform on large genomes. We recommend using it to compare smaller regions only (< 500 Kb).

Save As: This changes the location of where your figure will be created. Changing this after your figure has been created will not save it again under the new name.

File type: Easyfig figures may be saved as Bitmap (bmp) or Scalable vector graphics (svg). SVG files require an image viewer such as photoshop or GIMP, but are much better quality than bmp files and easier to manipulate. We recommend Inkscape, a free open source image editor for viewing and manipulating SVG files. Figures may also be previewed by selecting preview as a filetype. 1:1 shows the image at designated size (1 pixel in image = 1 pixel on screen). Shrink fits the image to screen. Colours may not be accurately reproduced due to shortcomings of Tkinter.

Create Figure: Creates the figure at the location specified in Save As. Will overwrite previous figures without warning

File: For saving and loading settings or preferences

Image: Access windows for modifying the figure being created

Blast: Access options to manually or automatically download BLAST

Help: Information about using and referencing Easyfig

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  1. Home
  2. Installation
  3. Windows
  4. OSX
  5. Linux
  6. Setting up Easyfig to automatically generate BLAST
  7. Tutorials
  8. Example 1
  9. Example 2
  10. Features of Easyfig
  11. Main screen
  12. Figure
  13. Subregions
  14. Annotation
  15. Legends
  16. Blast
  17. Graph
  18. Running from the command line
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