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

Release v1.5.0

• Ported to Python 3, no longer supports Python 2
• Added pythonic logging and argument parsing
• Merged build instructions for macOS and Unix
• Switched FastTree to RaxML
• All dependency tools must be on the system path (no longer defaults to bin/)
• More robust error checking (skips bad files instead of crashing, more warnings + debug mode)
• Fixed .gbk parsing
• Convenient input now allows sequences to be supplied via regex i.e. what use to be parsnp -d ref/ -r ! can now be written as parsnp -d ref/*.fna which allows for heterogeneous input directories and spread out data.

Test release of v1.5

v1.5beta

update tag

v1.2

Bug fixes

• Important fix to FastTree2 binary to enable use of double precision branch lengths (instead of minimum length of 0.0001); FastTree2 issue fully detailed in the following blog post: http://darlinglab.org/blog/2015/03/23/not-so-fast-fasttree.html.

v1.1.1

Fix to fully disable/deprecate -R parameter