As a result, methods based on the duplication-loss model perform poorly and cannot be used for gene trees affected by transfer.
RaxML is one of the most widely used phylogeny reconstruction programs, while NOTUNG and TreeFix are two well-known species tree aware gene tree error-correction methods based on the duplication-loss model.
Methods that only model duplication-loss are ineffective: Gene tree error-correction methods based on the duplication-loss model are ineffective at inferring gene trees affected by transfer, with average NRFD over all datasets of 0.088 (NOTUNG) and 0.079 (TreeFix).
Almost all existing species tree aware gene tree inference methods are based on the duplication-loss reconciliation model (Åkerborg et al., 2009; Durand et al., 2006; Górecki and Eulenstein, 2011; Rasmussen and Kellis, 2011; Vilella et al., 2009; Wu et al., 2013).
Genes were separated into four groups based on the gene duplication states: (1) one-to-many, (2) one-to-one, (3) many-to-many, and (4) new gene (no ortholog in the zebra fish genome).
Consider the problem of constructing a species tree from conflicting gene trees based on the gene duplication optimality criteria.
Based on the genome duplication history and number of synonymous nucleotide substitutions, the molecular-clock rate has been calculated to be faster in Arabidopsis than in Populus[ 33].
Based on the tandem duplication hypothesis, we also investigated whether the sequence similarity is higher for any mature sequence pairs with different pre-microRNA identifiers (all alignments are available in Additional file 4).
The third and probably the most accepted explanation for the origin of microRNAs is based on the inverted duplication of genes, which when transcribed would form hairpin structures capable of generating small RNAs with perfect complementarity to the parental transcripts (Allen et al. 2004; Axtell and Bowman 2008).
Many of these methods have been based on the probabilistic duplication-loss model, which describes how a gene-tree evolves over a species-tree with respect to duplication and losses, as well as extension of this model, e.g., the DLRS (Duplication, Loss, Rate and Sequence evolution) model that also includes sequence evolution under relaxed molecular clock.
