BuscoPhylo

Thanks to the advances in DNA sequencing technolgies, thousands of genome sequences of living organisms are being released in the public databases every day. BuscoPhylo has been implemented to provide a fully automated and complete pipeline to quickly perform BUSCO-based phylogenomic analysis starting from assembled genome sequences as inputs. BuscoPhylo is a free, on-line and user-friendly webserver accepting genome sequences in FASTA format as inputs and enabling to the user to export the tree ready for publication and all the results of the steps included in the pipeline for downstream analyses.

BuscoPhylo workflow

graph TD

    a{{Genome sequences >= 4 <br> <i>FASTA format}} -- <i>BUSCO --> b(BUSCO outputs)
    b --> c(Get Shared single copy BUSCO genes)
    c --> |<i>muscle & trimAl| d(Individual alignments <br> for each BUSCO family gene)
    d -- <i>Seqkit --> e(Concatenate alignments)
    e --> |<i>Infering tree using <br>IQ-TREE| f(ML tree)
    f --> |<i>ETE3| g[Graphical Display]
    f --> h[Download Results]

        classDef green fill:#93FF33,stroke:#333,stroke-width:2px
        classDef blue fill:#00FA9A,stroke:#333,stroke-width:4px

        class g,a,h green
        class b,c,d,e,f blue

Installation

1. Download the application and extract the zipped file in your web server (xampp, ampps, WAMP, online server …)

   # Download the BuscoPhylo source code 
   git clone https://github.com/alaesahbou/BuscoPhylo.git
   # Move the the BuscoPhylo dir to your your server (exmaple here lampp)
   mv BuscoPhylo/ /opt/lampp/htdocs/

2. Setup the server

   # Give BuscoPhylo root privileges using the following command
   sudo chown -R daemon /BuscoPhylo_directory
   sudo visudo
   # insert th following lines after User privilege specification comment 
   # for xampp replace USER by daemon and for ampps replace USER by ampps
   [USER] ALL=(ALL:ALL) ALL
   [USER] ALL=(ALL) NOPASSWD: ALL
   # open the file with a text manger
   vim /etc/php5/cli/php.ini
   # change these lines:
   max_file_uploads=5000
   upload_max_filesize=8000M
   post_max_size=8000M

3. Open BuscoPhylo tool via localhost on you browser (http://localhost/BuscoPhylo/)
4. Connect BuscoPhylo to mysql
   
   Enter your login and password of your mysql server
   
   

   Requirements

   • Python3( sudo apt install python3)
   • Busco(conda install -c bioconda busco)
   • Biopython(conda install -c conda-forge biopython)
   • MUSCLE(conda install -c bioconda muscle)
   • trimAl(conda install -c bioconda trimal)
   • IQ-TREE(conda install -c bioconda iqtree)
   • ETE3(conda install -c etetoolkit ete3)

from buscophylo import BuscoPhylo

buscophylo = BuscoPhylo()
buscophylo.Token("YOUR_API")
buscophylo.Project_Name("Project_Name")
buscophylo.lineage("Lineage")
buscophylo.mode("Mode")
buscophylo.directory("Directory")
buscophylo.Project_groupe("outgroup") # optional
buscophylo.run()