PhyloPhlAn2¶
Description¶
In PhyloPhlAn2 the markers database used to extract the phylogenetic signal can be either one of the two provided: PhyloPhlAn and AMPHORA2, or one defined by the user. For the correct working of PhyloPhlAn2, a script that format the database to be used by PhyloPhlAn2 is provided. The phylogenetic pipeline can be entirely configured through a set of input parameters and a configuration file (scripts are provided to generate different configuration files to perform different phylogenetic analysis) where the user can specify the preferred software to be used to perform each step of the pipeline. In addition, several parameters can be used to define whether to apply trimming and subsampling of the alignments produced, for instance, the type of trimming, the function to use to score the multiple-sequence alignments and the function that selects how many position to consider for each of the multiple-sequence alignment.
Environment Modules¶
Run module spider phylophlan2 to find out what environment modules are available for this application.
Environment Variables¶
- HPC_PHYLOPHLAN2_DIR - installation directory
- HPC_PHYLOPHLAN2_BIN - executable directory
- HPC_PHYLOPHLAN2_DOC - documentation directory
- HPC_PHYLOPHLAN2_EXE - examples directory
Categories¶
phylogenetics