PanPhlAn version history - SegataLab/panphlan GitHub Wiki

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
• panphlan_profile.py : input can be a directory or a text file containing path of input files

• Database of pangenomes added. Script for easy download : panphlan_download_pangenome.py. The database contains more than 3,000 species pangenomes, gene locations, and bowtie2 indexes
• Add script panphlan_find_gene_grp.py for finding potential mobile elements using the presence/absence matrix built

• Designed to work with Python 3; Python 2.7 compatibility is not guaranteed.
• Major changes in panphlan_pangenome_generation.py. It now works using ChocoPhlan and only generates bowtie2 indexes
• panphlan_old_pangenome_generation.py works as in the previous version. For custom database generation using usearch
• panphlan_profile.py add arguments to map genes ID to functionnal annotation data

• panphlan_pangenome_generation.py Roary clustering is accepted as input for database generation (instead of usearch7 clustering)

• panphlan_pangenome_generation.py gff gene-annotation files are accepted as input for database generation (instead ffn gene sequence input)

• Stable release published together with the PanPhlAn paper in Nature Methods (March 2016)

• panphlan_pangenome_generation.py gene-names are no more restricted to NCBI coding
• panphlan_profile.py set 2X as default min coverage threshold of a strain in sample

• First release of PanPhlAn as used for the analysis in the PanPhlAn paper