fixation-index-matrix [artifact]


A TXT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

Back to the main page of anvi’o programs and artifacts.

Provided by


Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.


A fixation index matrix is what it sounds like (a matrix of fixation indices) and is generated by anvi-gen-fixation-index-matrix.

This is a distance matrix where each column represnts a metagenome/sample and each row represents a metagenome/sample, so each cell represents the fixation index between two samples. The fixation index is a number from 0 (maximum similiarity) to 1 (maximum distance).

This is a form of view-data, so it can be provided to anvi-matrix-to-newick as is done in the Infant Gut tutorial.

For example, here is the fixation index matrix based off of a few random genes (1, 2, 3, 5, 6, 7, 8, 9, 21, 32, 35, 56, 567) in the infant gut tutorial:

           DAY_15A               DAY_15B                DAY_16                 DAY_17A                 DAY_17B               DAY_18                  DAY_19                  DAY_22A                 DAY_22B                DAY_23                  DAY_24
DAY_15A    0.0                   0.04918776635439459    0.11098963862572608    0.047199977957045336    0.0                   0.08439930158545839     0.06141920095408482     0.09624218229853498     0.0                    0.04711838006230529     0.08709060259498314
DAY_15B    0.04918776635439459   0.0                    0.07095764349628797    0.04742239843190177     0.04918776635439459   0.058754132113538526    0.012860485049109083    0.056111593790529324    0.04918776635439459    0.012757678005705375    0.05031628777187558


Edit this file to update this information.