PhyloExplorer automates this task by providing a feature to get available pictures from Wikispecies for all terminal taxa of an input tree or tree collection and for all taxa of a taxon list.
The user can then perform several operations on the input collection, such as: browsing the taxonomy excerpt corresponding to each input tree; restricting its trees to a subset of species by a simple mouse click; mining a relevant subset of trees through a simple querying language; and locating trees in TreeBASE matching taxa of the input collection.
Affinity graphs set aside questions of phylogeny in favour of capturing strong relationships among a set of input taxa.
For maximum-parsimony analysis, we used tree bisection/reconnection branch swapping, 25 random additions of input taxa, and 1,000 bootstrap replicates to assess node support.
(Lemmas 4.2, 4.3, 4.7 [ 3]) Let M be a set of input taxa with at most three states per character, and suppose G(M) is properly triangulatable.
Let M be a set of input taxa with at most three states per character, and consider any three characters χ i, χ j, χ k in M. If the partition intersection graph G(χ i, χ j, χ k ) is properly triangulatable, then the only possible chordless cycles in G(χ i, χ j, χ k ) are chordless 4-cycles, with two colors appearing once and the remaining color appearing twice.
Parsimony phylogenetic reconstructions were performed using the PHYLIP [ 62] software package and subjected to 100 bootstrap replicates with 10 randomizations of taxa input order for each bootstrap.
The SVDquartets algorithm takes unlinked multi-locus data for a set of four taxa as input and assigns a score to each of the three possible quartet topologies.
There are different variants of grafting taxa onto input trees [ 27].
Both analyses were implemented in RASP [ 72] and required ultrametric trees and the present distribution of the extant taxa as input files.
