MetaPhlAn 1.7.7 released

[Nicola Segata]

Dear MetaPhlAn users,

 we have just updated the MetaPhlAn package to version 1.7.7. With respect to the last version announcement (1.7.4) these are the changes:

- [1.7.7] New supporting feature: MetaPhlAn output tables can now be converted to BIOM format for downstream additional analyses (e.g. with the Qiime suite) of the taxonomic abundance profiles (thanks to Sami Pietilä for implementating the metaphlan2biom.py script)

- [1.7.6] Notation bug fix: now supporting --input_type bowtie2out that need to be specified as --input_type blastout before

- [1.7.5] New supporting features:

                  "-t marker_pres_table" outputs the list of markers with non-null abundance (i.e. present in the sample). The threshold for presence/absence call is specified via "--pres_th"

                  "-t marker_ab_table" outputs the normalize marker counts (multiplied by 1,000). The value is normalized by the size of the metagenome (to compare samples with different sequencing depth) if --nreads is specified

And here are the other previous additions to the version series 1.7

- [1.7.4]  New supporting feature: the script metaphlan_hclust_heatmap.py in plotting_scripts/ allows you to generate hierarchical clustering and heatmap visualization of multiple MetaPhlAn profiles. See plotting_scripts/readme.txt for details

- [1.7.3] MetaPhlAn now accepts metagenomes from the standard input (when using BowTie2). When passing the input from the standard input, it is now required to specify the input type ('multifasta', 'multifastq', or 'blastout'). When using a file as input, the input type is still guessed by MetaPhlAn automatically

- [1.7.2] multiple MetaPhlAn output obtained on distinct samples can now be easily merged into a unique "microbial clades vs samples" abundance table using the merge_metaphlan_tables.py script in the "utils" folder (thanks to Tim Tickle)

- [1.7.2] the MetaPhlAn output can now be visualized with Krona and with other software supporting the PhyloXML format, using the scripts in the "conversion_scripts" folder (thanks to Daniel Brami and James Taylor)

- [1.7.1] two aspecific genes removed from the database (thanks to Nick Loman)

Let us know if you have any comment or question.

many thanks