MiniNJ

MiniNJ is a distance method for inferring an unrooted species tree from gene family trees. It is equivalent to NJst when all gene families are single-copy gene families (at most one gene per species and per family), but performs better in presence of multiple-copy gene families. See our preprint for a complete description of the algorithm.

You can run MiniNJ from GeneRax/SpeciesRax. If you are interested in the MiniNJ tree only, it is simpler to run the executable njrax.

Running MiniNJ from GeneRax/SpeciesRax

When the executable generax is run with --species-tree MiniNJ, a MiniNJ tree is generated at species_trees/starting_species_tree.newick from the input gene trees (or from the gene trees inferred from the alignments).

Running MiniNJ from NJRax

njrax is a separate executable that is provided along with GeneRax. It implements NJst and MiniNJ. It takes as input:

• the name of the algorithm (MiniNJ or NJst)
• the path to the input gene trees file, that contains all the gene trees in newick format
• the path to the input mapping file, with the gene-species mappings for all the gene families (both Phyldog and Treerecs formats are supported)
• the path to the output species tree