Ruuning Phylosift on 4001 genome

[jitesh kumar]

Hie 

I have 4001 genome including MAGs derived from Anvio6 platform and NCBI genome. The HMM sources are as below:

HMM SOURCES COMMON TO ALL 4001 GENOMES

======================================================================================================

* Bacteria_71 [type: singlecopy] [num genes: 885]

* Archaea_76 [type: singlecopy] [num genes: 976]

* Protista_83 [type: singlecopy] [num genes: 1741]

* Ribosomal_RNAs [type: Ribosomal_RNAs] [num genes: 244]

Can i perform alignment of different sources (Bacteria, Archaea), with goal to make a microbial tree using Phylosift. 

Any manual or tutorials or advise exist pls share. I am new to phylosift.

Your help your be appreciated...

[Guillaume Jospin]

Yes, you can screen your genomes in --isolate --besthit mode which will generate a concatenation of 37 markers. You can then concatenate all your aligned sequence files for the concat marker (from you 4001 runs) to build a tree. You would have to start with fasta files for your MAGs.

GTDB-Tk does this all at once (instead of looping over 4k times) and uses a newer database of genes. It might be better suited for what you are looking for.

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