Ruuning Phylosift on 4001 genome

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jitesh kumar

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Apr 14, 2020, 1:57:44 PM4/14/20
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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

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Apr 14, 2020, 6:48:40 PM4/14/20
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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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