PhyloPhlAn 3.0 release and closure of PhyloPhlAn Google Group

[fasnicar]

Hello everyone,

The PhyloPhlAn repository has been migrated to GitHub due to the discontinued support of mercurial in Bitbucket.

The new repo URL is https://github.com/biobakery/phylophlan.

With this migration, we also officially release the new PhyloPhlAn 3.0 that can be easily installed from the Bioconda channel using conda:

conda install -c bioconda phylophlan

If you’re interested in a pre-print of the PhyloPhlAn 3.0 manuscript that is currently under review, please email us and we can send you a copy.

Very briefly, the main improvements of the PhyloPhlAn 3.0 are:

• Scale-up to very-large phylogenies (>10,000 genomes)
• Six presets for the most common phylogenetic analysis scenarios based on expected diversity of the genomes to analyze (--diversity [low|medium|high]; "low": for genus-/species-/strain-level phylogenies; "medium": for class-/order-level phylogenies; "high": for phylum-/tree-of-life size phylogenies) and accuracy/speed (--accurate or --fast)
• Taxonomic assignment based on the SGB system of newly assembled MAGs
• Easier integration of external tools
• Possibility to perform concatenation or gene tree pipeline
• Internal quality control steps to allow to retain input genomes that met the quality criteria
• Internal quality control steps to allow to discard phylogenetic markers that did not meet the quality criteria
• Possibility to estimate mutation rates from the MSAs
• A complete suite of software tools to download reference genomes for 17,621 species (Archaea, Bacteria, and Eukaryota kingdoms) from GenBank
• An automatic approach to download pre-computed sets of UniRef90 proteins core for 18,131 species (Archaea, Bacteria, and Eukaryota kingdoms)

The user manual and a complete set of tutorials are available here https://github.com/biobakery/phylophlan/wiki and here https://github.com/biobakery/biobakery/wiki/PhyloPhlAn, respectively.

We will continue to provide support and bugfix using both the GitHub issues tracker: https://github.com/biobakery/phylophlan/issues, as well as the new bioBakery help forum: https://forum.biobakery.org, which will replace the PhyloPhlAn Google Group that will be closed on May 4th, 2020.

Many thanks to all of you that used PhyloPhlAn so far providing over the years useful feedback, and we hope you find the new implementation easier to use for all your phylogenetics analyses.

Best regards,

Francesco Asnicar