v1.4.1

Changes:

- Uses pyproject.toml instead of setup.py for installation
- update minimal requirement for ncbi_genome_download to be compatible with the last NCBI format (issue #42)
- use --amino option for mafft protein alignements in order to force sequence type to be proteic and deal with ambiguous aa (see https://github.com/gem-pasteur/PanACoTA/commit/728445dd84f8b5d159c97371ee828ea8761ea938#commitcomment-122306169)
- fix issue with protein names. They must fulfill the conditions described in https://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/usage.html#protein-files

v1.4.0

- general: count available cpus instead of total cpus
- all: fixes in config file parameters
- prepare: option for single strain id
- annotate: fix in gff3 header
- annotate: fix in replicons header
- tree: option to write distance matrix with fastME

version 1.3.1
- fix issue 16: bootstraps from "all" module

version 1.3.0

-fix issue 11
- fix issue 14
- add TEST parameter to IQtree
- add proteic alignments if asked
- change pangenome filename format
- coregenome: possibility to give a subset of genomes
- align: take into account gembase complete genomes format

version 1.2.0

- prodigal train
- 0 included for mash distances
- configfile for 'all' module
- add choice genbank/refseq
- add ncbi taxid

version 1.1.0

- new module to run all modules: 'all'
- fix bug when there is a binary file in the genomes folder
- iqtree2 is by default

version 1.0.1: CHANGES

- fix bugs while formatting genomes annotated by prokka
- new option to select assembly level to download from NCBI

version 1.0