minor edits

README.md

@@ -481,7 +481,7 @@ Heatmap dimensions (default: 10 x 10) can be modified with the `--hheight` and `
 
 Unless the `--no_circos` command line switch is invoked, [Circos](https://circos.ca/) (concatenated and/or pairwise) will be generated from the protein clusters identified with SYNY (e.g. `.gap_0.`) and/or from the genome alignments computed with minimap2 (`.mmap.`).
 
-In the pairwise plots (`--circos pair`, set as default), genomes are plotted in pairs (query <i>vs.</i> subject) using the query as the reference. In the concatenated plots (`--circos cat`), all genomes are plotted together in a single figure, using the reference genome specified with the `--ref` command line switch. If omitted, the first genome encountered alphabetically will be used as the default reference. Both contenated and pairwise plots can be generated with the `--circos all` command line switch.
+In the pairwise plots (`--circos pair`), genomes are plotted in pairs (query <i>vs.</i> subject) using the query as the reference. In the concatenated plots (`--circos cat`), all genomes are plotted together in a single figure, using the reference genome specified with the `--ref` command line switch. If omitted, the first genome encountered alphabetically will be used as the default reference. Both contenated and pairwise plots can be generated with the `--circos all` command line switch (set as default).
 
 Two circos plots, `.normal` and `.inverted`, will be generated for each approach. In the inverted plots, the contigs/chromosomes from the genome(s) being compared to the reference are plotted in reverse, from last to first.
 
@@ -755,7 +755,7 @@ GPK93_01g00270  -       J0A71_11g23150  -
 
 In the above [Circos](https://circos.ca/) plot, links between the reference and the queried genomes are color-coded based on the reference genotype; links between the queried genomes are shown in light gray. In these plots, each chromosome/contig is plotted as a distinct [ideogram](https://circos.ca/documentation/tutorials/ideograms/ideograms/).
 
-Note that while SYNY can plot multiple genomes together in a single figure with `--circos cat` / `--circos all`, adding too much data can quickly clutter the Circos plots generated (drawing too many ideograms can make the figure illegible). If too dense, drawing pairwise plots with `--circos pair`( set as default) rather than concatenated ones should help with readability. However, when comparing genomes featuring many chromosomes/contigs, cluttering can also occur even when performing pairwise genome comparisons.
+Note that while SYNY can plot multiple genomes together in a single figure with `--circos cat` / `--circos all`, adding too much data can quickly clutter the Circos plots generated (drawing too many ideograms can make the figure illegible). If too dense, drawing pairwise plots with `--circos pair` rather than concatenated ones should help with readability. However, when comparing genomes featuring many chromosomes/contigs, cluttering can also occur even when performing pairwise genome comparisons.
 
 #### Custom Circos colors
 Custom colors for [Circos](https://circos.ca/) plots can be loaded directly from tab-delimited text files containing color names and their associated RGB values (see [custom_color_1.txt](https://github.com/PombertLab/SYNY/blob/main/Circos/custom_color_1.txt) for an example). A few custom presets are also available to use in SYNY.