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  • v1.4.1
    - Uses pyproject.toml instead of 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
    - fix issue with protein names. They must fulfill the conditions described in
  • v1.4.0
    1ee65c56 · version 1.4.0 ·
    - 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
  • v1.3.1
    499ef229 · version 1.3.1 ·
    version 1.3.1
    - fix issue 16: bootstraps from "all" module
  • v1.3.0
    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
  • v1.2.0
    version 1.2.0
    - prodigal train
    - 0 included for mash distances
    - configfile for 'all' module
    - add choice genbank/refseq
    - add ncbi taxid
  • v1.1.0
    215f9199 · v1.1.0 ·
    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
  • v1.0.1
    7f1878d8 · add prepare func tests ·
    version 1.0.1: CHANGES
    - fix bugs while formatting genomes annotated by prokka
    - new option to select assembly level to download from NCBI
  • v1.0
    8e5d8f61 · Eduardo -> add P.C. ·
    version 1.0