3.2.1

• Fixes python compatibility, dependency and packaging issues of 3.2.0

3.2

• Updated phylophlan_assign_sgbs using MASH and skani for more precision and nicer verbose output
• Added phylophlan_patristic_distances script for fast calculation of leaf-to-leaf distance matrix

3.1.1

• Fixes non-verbose execution bug when running phylophlan_assign_sgbs.py (previously phylophlan_metagenomic.py)

3.1

• Phylogenetic pipeline in phylophlan.py improved thanks to users' feedback
• Taxonomic assignment of genomes and MAGs via phylophlan_assign_sgbs.py (previously phylophlan_metagenomic.py) improved with databases synced with MetaPhlAn and faster

3.0.3

• Fixing and improving folders check, params in exception, empty MSA check, and input handling
• adding the --convert_N2gap param

3.0.2

• Downloads now from http://cmprod1.cibio.unitn.it
• Added sanity checks for the gene tree pipeline
• Added warning message when specifying ASTRAL in the config file generator as it should be manually configured

3.0.1

version 3.0.1 also in setup.py

3.0

PhyloPhlAn 3.0

See readme for more information

1.0

Please use one of the following two links for downloading PhyloPhlAn 1.0

• phylophlan-1.0.zip
• phylophlan-1.0.tar.bz2

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NB: Please do not use the automatic links generated by GitHub below.