… of branches S … S is the smallest set of edges which, by definition, must be part of the speciation
process. Figure 1 illustrates the algorithm for a triplet of nodes u, v, w, and marks the set S …

… bifurcating tree T ′ s by pruning subtrees from T such that the ASV of T ′ s is maximized.
If… tree T ′ s remains unrooted. In particular, all internal nodes of T ′ s have three outgoing …

… mode: let G be a GFT and S a species tree. We replace the reconciliation likelihood term
L(S, G) by L(S′, G), where S′ is obtained from S by pruning all species that are not covered …

… set of the reference tree S(|$T_{R})$| should be equal to the union of the taxon sets of
all evaluation trees S(|$T_{E})$|. All evaluation trees may have the same taxon set as S(|$T_…

… Filtering move candidates: In order to determine the most promising move candidate(s) and
accelerate move candidate evaluation, we apply a three-stage pre-filtering process: we filter …

Motivation Recently, Lemoine et al. suggested the transfer bootstrap expectation (TBE)
branch support metric as an alternative to classical phylogenetic bootstrap support for taxon-rich …

… (s) table(s) from spreadsheet editors such as Microsoft EXCEL and save it (them) into a
single SPART file. A new software tool named SPARTMAPPER has also been developed (…

… The taxon set of the reference tree S(T) should be equal to the union of the taxon sets of all
evaluation trees S(T̂). All evaluation trees may have the same taxon set as S(T̂) (eg, T and …

… Again, s k and t k are the values for a given branch with index k, of two given trees S and T as
… of s k and t k . This ensures that the metric produces well-defined values in cases where t k …

… matching algorithms we direct the interested reader to Faro’s and Lecroq’s review article [11]. …
the benefits of these approaches by using modern processor’s SIMD extensions [9, 19]. …