A tool for quickly and accurately classifying fungal genomes
This soft extends the phylophenetic concept of species for its application in the classification of fungal genomes. It evaluates several working hypotheses:
Genomic coherence, monophyly, and the speciation or coalescence hypothesis under the Bayesian model of Poisson tree processes (bPTP). This allows the evaluation of phenetic, genomic, phylogenetic and evolutionary-molecular elements in a corpus of speciation.
Usage: ./fclassifier.sh -i <input_file> -d <database_file> -m <model>
Options:
-i <input_file> Input fasta, fna, or fa archive
-d <database_file> Database file in .msh format
-m <model> Select between two species delimitation methods mptp or bptp
-h Display this help message
More information on the species delimitation methods here mPTP or bPTP
I strongly recommend testing both speciation models (mptp and bptp)
Before you begin, install the following dependencies:
you might want to try mamba instead of conda in the following commands
sudo apt install apcalc
sudo apt install ncbi-entrez-direct
sudo apt install ncbi-blast+
sudo apt-get install -y mptp
conda install -c bioconda fastani
conda install -c bioconda jolytree
conda install -c bfurneaux bptp
Download preconfigured Fungal database here Fungal Mash DB
Contact: Ayixon Sánchez-Reyes ayixon@gmail.com
Computational Microbiology
Microbiological Observatory
Institute of Biotechnology, UNAM, Cuernavaca, MEXICO
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= VERSIONS = VERSION=1.0. Written by Ayixon Sánchez Reyes