MAGELLAN

Maps of Genetical Landscapes

Sections

   General
   Navigation
   Visualization
   Models
   File Format
   Sources and executables
   FAQ

General

MAGELLAN is an integrated tool to visualize and analyze fitness landscapes of small dimension (up to 7-8 loci). It was primarily developed in the years 2012-2014 by S. Brouillet and G. Achaz for personal use, but was subsequently made public so that other users could benefit from the work. S. Matuszewski has implemented all the multiallel landscape statistics in 2016, H. Annoni designed the final look, and L Ferretti participated in the general development.

Although still unpublished, MAGELLAN should be submitted for publication in the near future. For now, if you use MAGELLAN, please cite: MAGELLAN: a tool to explore small fitness landscapes. S Brouillet, S Matuszewski, H Annoni, L Ferretti and G Achaz. In prep.

We would be very happy to receive suggestions for improvement for MAGELLAN. If you have any comment, suggestion or bug report, or if you want to be kept informed about possible updates, please contact G Achaz.

Navigation

MAGELLAN has 3 main pages. To access the general menu, click on the MAGELLAN logo (upper left). From there, you can:

  1. Generate fitness landscapes using theoretical models
  2. Browse the published experimental landscapes
  3. Visualize your own landscape, provided it is given in the appropriate format (see below).

All subsequent pages have sub-menus that are accessible through tabs navigation.

A dynamical visualization

All representations are based on a reference genotype that is placed on the left. All gentoypes are subsequently placed to the right at a distance that is their hamming distance (number of different loci) to the reference. Once a landscape is pictured, a sub-menu of 4 tabs is displayed:
  1. Landscape: pick another experimental landscape or (re)draw a new model landscape. If the landscape was generated by a model, this menu can be used to select a different model (New) or to redraw a new realization of the same model (Redraw).
  2. View/draw: customize the visualization (rotate landscape, log/linear scale, zoom, display/hide specific paths, ...) After any modification of this page, you have to click the "Draw" button. "Clear" will reset to default parameters. Parameters include:
  3. Save is used to save the current picture. At the moment, output format are either svg or pdf
  4. Stats displays classical summary statistics for the current visualization. Summary statistics reported here are reviewed in Szendro et al., 2013, as well as Ferretti et al., submitted.

Model fitness landscapes

Whatever model is chosen, you must specify the number of loci, and the number of alleles per locus (that can be identical or variable for all loci ). Several classical models of fitness landscapes are provided, those reviewed in Ferretti et al., in prep. If mean/variance values are set to -1, uniform [0,1] random variable are drawn. Otherwise, we use Normal (μ,σ) deviations.

File Format

The first line sets the number of alleles for each locus. Therefore, it has L columns separated by spaces, where L is the numbers of loci.

Each subsequent line represents a genotype (a sequence of alleles) followed by the associated fitness value. Further information may be added after the fitness values, which is ignored.

A file for 3 loci with 2 alleles each would look like:
#description of landscape on one line; must begin by '#' (this line is optional) 2 2 2
0 0 0 0.5
0 0 1 0.7
0 1 1 0.2
0 1 0 1.2
1 0 1 1.3
1 1 0 5
1 0 0 0.7
1 1 1 7.1

Sources and executables

Magellan command line source code can be dowloaded here

You can also download a set of executable binaries for

FAQ