text: user2572: Does anyone know of a good tool for visualizing gene loci? Basically, I'd like to show how a group of genes look in different strains of a bacteria. I have annotation of course, I just need a tool to plug it into and get an image of the locus to compare.
  I'm talking something basic like this:
  
  
  user298: GFF2PS was developed for exactly this sort of thing. It takes a GFF file as input, and will produce a pretty PS output showing the annotations. It was used to create the poster for Celera's human genome draft [1]. 
  Here's a very simple example of what it can do:
  
  And a more complex one from the mosquito genome paper [2] (click here for a full size, 1.5M gzipped PostScript file):
  
  If you are happy with the defaults, it is very easy to use, but otherwise it is a bit of a pain to configure. It is absurdly powerful though. 
  
  
  Venter et al. Science 291(5507):1304-1351 (2001)
  Holt et al. Science 298(5591):129-149 (2002)
  
  
  user2572: I ended up using Easyfig, which is made for the task and requires little tinkering around, once fed the genbank files.
  (Granted, being so simple, it's hard to make the image more advanced, but it serves my purposes for now).
  
  Here's an example of my image.
  
  user10434: gggenes is a ggplot2 based solution and looks very appealing. Plus, it has a nice introduction with examples.
  library(ggplot2)
  library(gggenes)
  ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
    geom_gene_arrow() +
    facet_wrap(~ molecule, scales = "free", ncol = 1) +
    scale_fill_brewer(palette = "Set3") +
    theme_genes()
  
  
  
  user939: I think in R, Gviz is the best choice. I have used it for human sequences but it will probably also be suitable for Prokaryotes.
  Another option is MS powerpoint, if you only need the arrows...
  
original_text: 2572: <p>Does anyone know of a good tool for visualizing gene loci? Basically, I'd like to show how a group of genes look in different strains of a bacteria. I have annotation of course, I just need a tool to plug it into and get an image of the locus to compare.</p>
  
  <p>I'm talking something basic like this:</p>
  
  <p><a href="https://i.stack.imgur.com/CPGkw.gif" rel="noreferrer"><img src="https://i.stack.imgur.com/CPGkw.gif" alt="enter image description here"></a></p>
   298: <p><a href="http://big.crg.cat/services/gff2ps" rel="nofollow noreferrer">GFF2PS</a> was developed for exactly this sort of thing. It takes a GFF file as input, and will produce a pretty PS output showing the annotations. It was used to create <a href="http://science.sciencemag.org/content/suppl/2001/02/10/291.5507.1304.DC2" rel="nofollow noreferrer">the poster</a> for Celera's human genome draft <a href="http://www.sciencemag.org/cgi/content/abstract/291/5507/1304" rel="nofollow noreferrer">[1]</a>. </p>
  
  <p>Here's a very simple example of what it can do:</p>
  
  <p><a href="https://i.stack.imgur.com/DrQxG.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/DrQxG.png" alt="gff2ps example"></a></p>
  
  <p>And a more complex one from the mosquito genome paper <a href="http://www.sciencemag.org/cgi/content/abstract/298/5591/129" rel="nofollow noreferrer">[2]</a> (click <a href="http://genome.imim.es/references/genome_maps/2002_Science_v298_i5591_p129_fig1_MosquitoGenome.ps.gz" rel="nofollow noreferrer">here</a> for a full size, 1.5M gzipped PostScript file):</p>
  
  <p><a href="https://i.stack.imgur.com/twKYV.jpg" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/twKYV.jpg" alt="anopheles gambiae genome"></a></p>
  
  <p>If you are happy with the defaults, it is very easy to use, but otherwise it is a bit of a pain to configure. It is absurdly powerful though. </p>
  
  <hr>
  
  <ol>
  <li><a href="http://science.sciencemag.org/content/suppl/2001/02/10/291.5507.1304.DC2" rel="nofollow noreferrer">Venter et al. Science 291(5507):1304-1351 (2001)</a></li>
  <li><a href="http://www.sciencemag.org/cgi/content/abstract/298/5591/129" rel="nofollow noreferrer">Holt et al. Science 298(5591):129-149 (2002)</a></li>
  </ol>
   2572: <p>I ended up using <a href="http://mjsull.github.io/Easyfig/" rel="nofollow noreferrer">Easyfig</a>, which is made for the task and requires little tinkering around, once fed the genbank files.
  (Granted, being so simple, it's hard to make the image more advanced, but it serves my purposes for now).</p>
  
  <p><a href="https://i.stack.imgur.com/ARj7n.gif" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/ARj7n.gif" alt="Easyfig example from the homepage."></a></p>
  
  <p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498615/bin/12864_2019_5692_MOESM4_ESM.pdf" rel="nofollow noreferrer">Here's an example of my image.</a></p>
   10434: <p><a href="https://github.com/wilkox/gggenes/" rel="nofollow noreferrer">gggenes</a> is a ggplot2 based solution and looks very appealing. Plus, it has a nice introduction with <a href="https://wilkox.org/gggenes/articles/introduction-to-gggenes.html" rel="nofollow noreferrer">examples</a>.</p>
  <pre class="lang-r prettyprint-override"><code>library(ggplot2)
  library(gggenes)
  ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
    geom_gene_arrow() +
    facet_wrap(~ molecule, scales = &quot;free&quot;, ncol = 1) +
    scale_fill_brewer(palette = &quot;Set3&quot;) +
    theme_genes()
  </code></pre>
  <p><img src="https://wilkox.org/gggenes/articles/introduction-to-gggenes_files/figure-html/theme_genes-1.png" alt="" /></p>
   939: <p>I think in R, <a href="https://bioconductor.org/packages/release/bioc/html/Gviz.html" rel="noreferrer">Gviz</a> is the best choice. I have used it for human sequences but it will probably also be suitable for Prokaryotes.</p>
  
  <p>Another option is MS powerpoint, if you only need the arrows...</p>
  