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PhaME_m

The debugging version of PhaME (Phylogenetic and Molecular Evolution analysis tool). PhaME_m retains all the functions of PhaME, namely performing phylogenetic and molecular evolutionary analysis from sequencing reads, draft assemblies or completed genomes. The sequencing data in FASTQ or FASTA format can be directly inputted.

Why PhaME_m?

Since PhaME has not been updated for a long time, the existing versions (precompiled, development, and docker versions) have some issues on installation or running. PhaME_m debugs these issues. Following the installation guide below, the PhaME can be successfully installed and run on a local machine.

How to install?

  1. Create a separate conda environment and then activate it: 
    conda create -n phame_m
    conda activate phame_m
  2. Install required dependencies in the "phame_m" conda environment: 
    mamba install perl-bioperl
mamba install samtools
mamba install bcftools
mamba install mummer
mamba install bowtie2
mamba install fasttree
mamba install bbmap
mamba install raxml
mamba install perl-parallel-forkmanager
mamba install perl-statistics-distributions
mamba install paml
mamba install mafft
mamba install hyphy
  3. Clone the github repo of PhaME: 
    git clone https://github.com/LANL-Bioinformatics/PhaME.git
  4. Test if the installation was successful: 
    cd PhaME
bash ./test/TestAll.sh 1

How to run?

Please see steps.txt.
Note: If you want to know more details about PhaME, see the link https://phame.readthedocs.io/en/latest/index.html

FAQ

  1. ERROR: It makes no sense to perform bootstrap with less than 4 sequences.
  2. ERROR: Alignment must have at least 3 sequences.

More about PhaME:

  1. The github repo:
    https://github.com/mshakya/PhaME/tree/master
  2. Docs: https://phame.readthedocs.io/en/latest/index.html
  3. The publication:
    Shakya, M., Ahmed. S.A, Davenport K.W., Flynn M.C., Lo. C-C, Chain P.S.G. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Sci. Rep. 10, 1723 (2020).