v1.2.10

• added script panaroo-extract-gene to extract a fasta file given a gene name
• fix gene sequence prefilter for non-standard codon tables
• minor update to simulation script to work with new version of numpy
• minor fixes to pseudo_full_pangenome and filter_pa scripts

v1.2.9

• bug fixes for the spydrpick script
• fix for bug caused by case insensitive file labels in some OSX systems resulting in the program crashing when building the core genome alignment.
• added mamba installation to the docs

v1.2.8

• Adds support for different codon tables
• Updated panaroo-qc script to include the option not to produce the final plots
• Fixed minor bugs in the panaroo-fmg and panaroo-img scripts
• Fixed a major bug in the spydrpick script
• Fixed minor bug in the extractGeneRegionFromGMLGenes script
• Fixed rare bug that led to edges of the graph not being successfully causing the program to crash when saving the final .gml file

v1.2.7

• updated panaroo-msa to fix bug that caused it to crash when generating the full set of pangenome alignments
• updated documentation for thresholds which was out of date
• updated presence absence matrices to include isolate names in header
• added script to filter presence absence files
• fixed bug in generation of summary_statistics.txt file

v1.2.4

• added option to filter annotations that are not compatible with Panaroo due to premature stop codons or incorrect gene length
• removes a reference to the obsolete Alphabet module of biopython
• fixes a bug in the merge-graph script
• updated docs

v1.2.3

• fixed bug caused by commas in contig names
• added experimental code to merge graphs and added additional single genomes to an existing graph

v1.2.2

• updated panaroo-merge script
• updated get_gene_neighbors.py script and included it as one of the main scripts. It can now be run as panaroo-gene-neighbourhood
• updated documentation
• fixed a bug in the multiple sequence alignment script

v1.2.0

• panaroo now requires the --mode parameter to be specified explicitly
• speed improvements
• added the --length_outlier_support_proportion parameter to better handle spurious long annotations.
• bug fixes for the panaroo-spydrpick-runner script
• panaroo will now create the output directory if it does not already exist
• the delimiter between genes has now been updated to ~~~
• bug fixes for the get_neighborhood.py script
• minor updates to the documentation

v1.1.2

• bug fix for --merge_paralogs option
• added gene names to pan_genome_reference.fa file
• updated progress output to allow a 'quiet' mode

v1.1.0

• Significant speed improvement for large datasets
• Fixed minor issue with MSA generation of singletons
• Fixed issue with merging paralogs
• Updated installation documentation
• Formatted code using the 'yapf' format