BMGE
Description
Here is presented a new software, named BMGE (Block Mapping and Gathering with Entropy), that is designed to select regions in a multiple sequence alignment that are suited for phylogenetic inference. For each character, BMGE computes a score closely related to an entropy value. Calculation of these entropy-like scores is weighted with BLOSUM or PAM similarity matrices in order to distinguish among biologically expected and unexpected variability for each aligned character. Sets of contiguous characters with a score above a given threshold are considered as not suited for phylogenetic inference and then removed. Simulation analyses show that the character trimming performed by BMGE produces datasets leading to accurate trees, especially with alignments including distantly-related sequences. BMGE also implements trimming and recoding methods aimed at minimizing phylogeny reconstruction artefacts due to compositional heterogeneity.
Environment Modules
Run module spider BMGE to find out what environment modules are available for this application.
System Variables
- HPC_BMGE_DIR - installation directory
- HPC_BMGE_BIN - installation directory
Additional Information
You must add the HPC_BMGE_BIN prefix to the name of the JAR file when running the program. For example (using the built in help function):
java -jar ${HPC_BMGE_BIN}/BMGE.jar -?