PanPhlAn 3.1

Minor convenience update

• panphlan_download_pangenome.py now includes md5 checksum, automatic retries and automatic file removing after extraction
• panphlan_map.py : temporary location can be specified, output in no longer compressed by bz2 (more convenient to create tar.bz2 archives with all results )
• panphlan_profile.py : input can be a directory or a text file containing path of input files
• Removed panphlan_find_gene_grp.py as it was full of experimental and unfinished code
• Wiki and Tutorial updates

PanPhlAn 3.0.1

Update of the pangenome database

• Fix the duplicated sequences issue
• Add a md5sum check of the downloaded file

PanPhlAn 3.0

Main changes :

• PanPhlAn no longer supports Python 2, please update to Python 3

• panphlan_download_pangenome.py

  • Pangenome database has been extended and download is now easy
  • Pangenome folder now contain annotations tsv file mapping gene families (UniRef) to GO, KO, KEGG, Pfam, eggNOG...

• panphlan_find_gene_grp.py

  • First draft of automatic detection of gene families of interest in the profile matrix
  • Visualization of the profile matrix through clustered HeatMap

For question and discussion see the bioBakery forum

Legacy 1.3 version

Saving last updates of the 1.3 branch before replacing it with the PanPhlAn 3.0 version

1.3

Merge branch 'master' of https://github.com/SegataLab/panphlan