v1.6.0

• Added argument --family_len_dif_percent as an option to the merge graphs script as requested in #359
• Added argument --random_seed to specify random seed for the MDS quality control plot as requested in #314
• Updated to remove deprecated numpy function #351 and #352
• Fix for iterative GFF output #212

v1.5.2

• fixes a bug in the gff creation script
• removes deprecated plotly dependencies.

v1.5.1

• Added the option to specify 'none' as the aligner, allowing alignment to be run separately as requested in #306.
• Removed the dependency on the Bio.Applications module, which is going to be deprecated, addressing #301.
• Exposed the CD-HIT length requirement in the gene family clustering steps to address #299.
• Bug fixes to address #303.
• Updated GitHub Actions versions.

v1.5.0

• Adds an option to turn off gene re-finding completely. Users can now choose between three re-finding levels including the original, strict and off.
• Fixes bug #275, introduced in v1.4.0
• Now handles alternative start codons properly to address issue #274
• Improves multithreading for codon alignment thanks to @nzmacalasdair

v1.4.2

• Addresses bug highlighted in #269. This was introduced in v1.4.0
• Fixes a problem with genes with overly long names crashing the program

v1.4.1

• Update to ensure gffutils writes to the Panaroo temporary directory rather than the system temporary directory. Previously, this could cause issues when users had strict space requirements on the system tmp directory. It also increased the chance of a collision between temporary files when running multiple instances of Panaroo at the same time.

v1.4.0

Includes a number of updates and important bug fixes:

• New option to only use a random subset of genes for generating a core alignment thanks to @mgalardini
• New option to only consider valid genes (without stop premature codons and of correct length). Thanks to issue #263 raised by @NickJD
• Important fix to the panaroo-merge-graph script which had a bug that prevented the --merge-paralogs options from working. This is now the recommended way to run this script.
• Fixed bug in panaroo-integrate raised by @maxibor
• added warning if no matching sequences are found between the annotations and the corresponding fasta file/section
• added check for the number of core genes to prevent a crash if no clusters passed the core frequency threshold

v1.3.4

Fixes a number of minor issues:

• Fixes a bug in the post run alignment script panaroo-msa. This was encountered when not all input genomes were present in the generated pangenome graph.
• Now prints an informative message if there are no gene clusters that pass the core frequency threshold.
• Print a more informative error message if an invalid Genbank file is provided.

v1.3.3

This release fixes some minor bugs including in

• panaroo-extract-gene Fixes an issue caused by duplicate gene IDs appearing in separate genomes
• panaroo-merge Adds a missing parameter that was introduced in the recent release to generate filtered core genome alignments.

v1.3.2

This release fixes minor bugs and adds critical new functionality to generate an automatically filtered core genome alignment. We have found that this filtered alignment leads to superior phylogenetic trees.

• added new core genome alignment output that uses a Block Mapping and Gathering with Entropy (BMGE) filter to remove genes that are likely to cause issues when reconstructing phylogenies.
• fixed a bug that created many temporary files when using PRANK for gene alignment.
• fixed a bug in the extract gene post-processing script
• updated dependencies