The list of MPI software planned for installation¶

Assemblers / de novo (distributed)¶

•   ABySS (MPI) — short-read genome assembler (true multi-node).
•   HipMer / MetaHipMer (MPI/PGAS) — extreme-scale genome/metagenome assembly (NERSC/LBL).

Multiple sequence alignment (MSA)¶

•   MAFFT-mpi — MPI version for very large MSAs.
•   Clustal Omega (MPI build) — supports MPI when compiled with --enable-mpi.

Sequence search / homology¶

•   HMMER3 (MPI mode) — hmmsearch --mpi … for database partitioning across nodes.
•   PLAST (MPI) — parallel BLAST-like protein search at scale.
•   mpiBLAST (legacy) — BLAST database sharding across nodes.

Phylogenetics / phylogenomics¶

•   RAxML / RAxML-NG (MPI) — maximum-likelihood tree inference.
•   MrBayes (MPI) — Bayesian phylogenetics.
•   ExaML (MPI, legacy) — ML on very large alignments.
•   PhyloBayes-MPI — Bayesian inference for complex models.

Cryo-EM / structural biology¶

•   RELION (MPI+OpenMP) — 2D/3D classification/refinement at cluster scale.
•   AMBER (pmemd.MPI), LAMMPS (MPI), NAMD (MPI build) — MD engines widely used in biomolecular simulations.

Whole-genome comparison / other¶

•   MUSCLE-MPI (less common) — MPI variant used in some builds/pipelines.