MrBayes

AutoDock Vina — fast open-source molecular docking engine for predicting protein-ligand binding poses and affinities. Uses gradient-optimization conformational search with Vina, Vinardo, or AutoDock4

1 shared topic • 2 shared operations

BEAST2 — Bayesian Evolutionary Analysis by Sampling Trees. Cross-platform Java application for Bayesian phylogenetic inference using MCMC sampling. Use when estimating time-calibrated phylogenies, rel

1 shared topic • 2 shared operations

MDAnalysis — Python library for analyzing molecular dynamics trajectories and atomic coordinate data. Supports 40+ file formats (DCD, XTC, TRR, PDB, GRO, AMBER, LAMMPS). Provides RMSD, RMSF, hydrogen

1 shared topic • 2 shared operations

PhyML — maximum likelihood phylogenetic inference from nucleotide and amino acid sequence alignments. Supports GTR, HKY, K80, JC, and 15+ DNA/protein substitution models, gamma rate heterogeneity (+G)

1 shared topic • 2 shared operations

RAxML-NG — maximum likelihood phylogenetic tree inference using iterative SPR moves with libpll likelihood computation. Supports DNA, protein, binary, and multi-state data with partitioned analyses, n

1 shared topic • 2 shared operations