phylophlan IMG genome set download?

[RMondav]

Greetings and thanks for phylophlan!

I'm doing a compare and contrast between genome and 16S phylogenetic trees using phylophlan (+dependencies) for (MAG) genomes. I wanted to extract 16S sequences from the phylophlan genome files for the comparison but phylophlan has faa seqs only in its dataset. But, as the phylophlan dataset has IMG IDs, I should be able to download the genomes from IMG and extract the 16S rRNA genes.....but I can't find any command line option to download eg gbk files from IMG using the ID list. Is the phylophlan data collected in a 'genome set' on IMG that could be shared in a group? Is there some other way download all the genomes (or 16S genes) from IMG? If anyone's interested I could post the collated 16S gene seqs for other people to use in the future.

many thanks 

RMondav

[Francesco Asnicar]

Hi RMondav,

We don't have those genomes stored in a genome set collection. I have to say I haven't tested this, but if you look at the "ppafull.tax.txt" file (https://bitbucket.org/nsegata/phylophlan/src/1d174e34b2ae601c18d176e3b1f3d73125d46e5a/data/ppafull.tax.txt?at=default&fileviewer=file-view-default, inside the "data" folder in the PhyloPhlAn repository), the first column of the file (is tab-separated) should contain the ids you're looking for.

Please let me know you should need more info.

Many thanks,

Francesco

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