v1.7.1

• Mismatch=-4 and gap=-2 for extending LCBs
• Fixed bug that created extra gaps in LCB extension
• Fixed bug that resulted in FastTree being used in cases when it wasn't requested
• Fixed bug that duplicated reference in alignment output
• Reference sequence is now first in extended xmfa output

Release v1.7.0

• Added option --extend-lcbs which uses a naive alignment to extend the boundaries of clusters.

Release v1.6.2

• No longer deletes the core SNPs file, parsnp.snps.mblocks. Users can now use that file to run their own custom phylogenetic analysis using this file as input.

Release v1.6.1

• Fixes an issue where a list was compared to an integer.

Release v1.6.0

• Add --skip-phylogeny option to allow users to skip phylogeny reconstruction
• Add --validate-input option to allow users to validate files provided by -d with Biopython parsing

Release v1.5.6

• Add option to generate .vcf output via the --vcf flag
• Remove tmp/ directory in output folder

Release v1.5.4

• Fixes issue for multireference fastas mentioned in #87

v1.5.3

• Fixed memory limit in Muscle library so that multiprocessing doesn't crash
• Changed parsnp compilation to -O2 to fix WSL2 bug
• Added warning for trying to use too many threads

Release v1.5.2

• Fixed fallback to FastTree on RaxML failure
• Made --curate include all genomes regardless of length

Release v1.5.1

Bugfixes for Parsnp v1.5.0:

• Mash and FasANI recruitment now works regardless of reference type
• Phiprofile fixes for python 3
• Logging input errors is now cleaner