SYNY-v0.7e

• Added heatmaps displaying the percentages of proteins found in clusters between each pair of genomes (summarized in SYNTENY/clusters_summary_table.tsv)
• Fixed dotplot issue with unidimensional arrays.
• Fixed dotplot issue when the total number of subplots is 1; now generates a single plot instead of a subplot.

SYNY-v0.7d

• Now calculates pairwise genome alignment metrics from minimap2 PAF files, summarizes them as scatter plots, and stores the results in the ALIGNMENTS/METRICS subdirectory (see paf_metrics.py).
• Minor README restructuring to improve readability

SYNY-v0.7c

• Added a --resume option to skip previously computed minimap2 alignments ## Useful when optimizing barplots/dotplots
• Added dimensions to barplot/dotplot output file names ## To prevent overwriting previous files when optimizing plots
• Barplot/dotplot height/width options are now independent: --height/--dheight and --width/--dwidth

SYNY-v0.7b

• Added preset option for minimap2 (--asm 5, --asm 10 or --asm 20), default = off
• Added option to skip dotplots (--no_dotplot)
• Added option to adjust gaps in dotplots (--wdis / --hdis)
• Added options to adjust Circos ticks, ideograms, links and points per track max values

SYNY-v0.7

• Now generates barplots showing colinear blocks between compared genomes using a per contig/chromosome color palette (default) or using a monochrome color instead (with --monobar blue).
• Added a color palette option to dotplots (e.g. --dotpalette inferno)
• Minor code fixes

SYNY-v0.7a

• Reduced memory usage with paf_to_dotplots.py
• Added color scheme to barplot/dotplot output files
• Misc bug fixes

SYNY-v0.6b

• Cleaner dotplots
• Minor code fixes
• Better readme

SYNY-v0.6a

• Now generates pairwise genome alignment dotplots (in PNG format) from the minimap2 PAF files (using mathplotlib)
• Minor code fixes

SYNY-v0.6

• Added minimap2 dependency: now generates pairwise genome alignments in MAF, PAF and ALN (BLAST-like) formats
• Now generates colinearity plots from pairwise genome alignments (PAF) as well as from conserved protein clusters (SYNY)

SYNY-v0.5c

• Circos plots are now generated properly