Sub-tomogram image analysis of cryo-ET data was carried out with the Automated Recognition of Geometries, Objects, and Segmentations (ARGOS) software package (FEI Company, Hillsboro, Oregon, USA). For this analysis an 80 3 pixel subtomogram was extracted from a tomogram using the Chimera [53] software package. In this analysis the tomogram used contained a linear region of the Ebola virus ( Figure S4 ), and the 80 3 pixel sub-tomogram contained a single linear segment. This template was then used by the ARGOS software to conduct an exhaustive search of the original tomogram for similar structures. This analysis involved a six dimensional search matrix (three positional variants, and three rotational variants). The entire search process was sped up by the ARGOS software by utilizing parallel processing on the computer's graphics processing unit (GPU). Once individual sub-tomograms were selected based on correlation, they were inspected and compared to the initial template sub-tomogram. The extracted and aligned sub-tomograms were subsequently averaged with a filter that minimized the missing wedge artifact. This average structure then was used as the reference and the entire procedure was repeated several times.