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.
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.
- Create a separate conda environment and then activate it:
conda create -n phame_m
conda activate phame_m
- 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
- Clone the github repo of PhaME:
git clone https://github.com/LANL-Bioinformatics/PhaME.git
- Test if the installation was successful:
cd PhaME bash ./test/TestAll.sh 1
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
- ERROR: It makes no sense to perform bootstrap with less than 4 sequences.
- ERROR: Alignment must have at least 3 sequences.
- The github repo:
https://github.com/mshakya/PhaME/tree/master - Docs: https://phame.readthedocs.io/en/latest/index.html
- 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).