3,943 research outputs found
SunStar: an implementation of the generalized STAR method
Master's Project (M.S.) University of Alaska Fairbanks, 2017STAR ... is a method of computing species trees from gene trees. Later, STAR was generalized and proven to be statistically consistent given a few conditions (Allman, Degnan, and Rhodes 2013). Using these conditions, it is possible to investigate robustness in the species tree inference process, the lack of which will produce instabilities in the tree resulting from STAR. We have developed a software package that estimates support for inferred trees called SunStar
On the accuracy of language trees
Historical linguistics aims at inferring the most likely language
phylogenetic tree starting from information concerning the evolutionary
relatedness of languages. The available information are typically lists of
homologous (lexical, phonological, syntactic) features or characters for many
different languages.
From this perspective the reconstruction of language trees is an example of
inverse problems: starting from present, incomplete and often noisy,
information, one aims at inferring the most likely past evolutionary history. A
fundamental issue in inverse problems is the evaluation of the inference made.
A standard way of dealing with this question is to generate data with
artificial models in order to have full access to the evolutionary process one
is going to infer. This procedure presents an intrinsic limitation: when
dealing with real data sets, one typically does not know which model of
evolution is the most suitable for them. A possible way out is to compare
algorithmic inference with expert classifications. This is the point of view we
take here by conducting a thorough survey of the accuracy of reconstruction
methods as compared with the Ethnologue expert classifications. We focus in
particular on state-of-the-art distance-based methods for phylogeny
reconstruction using worldwide linguistic databases.
In order to assess the accuracy of the inferred trees we introduce and
characterize two generalizations of standard definitions of distances between
trees. Based on these scores we quantify the relative performances of the
distance-based algorithms considered. Further we quantify how the completeness
and the coverage of the available databases affect the accuracy of the
reconstruction. Finally we draw some conclusions about where the accuracy of
the reconstructions in historical linguistics stands and about the leading
directions to improve it.Comment: 36 pages, 14 figure
Inferring ancestral sequences in taxon-rich phylogenies
Statistical consistency in phylogenetics has traditionally referred to the
accuracy of estimating phylogenetic parameters for a fixed number of species as
we increase the number of characters. However, as sequences are often of fixed
length (e.g. for a gene) although we are often able to sample more taxa, it is
useful to consider a dual type of statistical consistency where we increase the
number of species, rather than characters. This raises some basic questions:
what can we learn about the evolutionary process as we increase the number of
species? In particular, does having more species allow us to infer the
ancestral state of characters accurately? This question is particularly
relevant when sequence site evolution varies in a complex way from character to
character, as well as for reconstructing ancestral sequences. In this paper, we
assemble a collection of results to analyse various approaches for inferring
ancestral information with increasing accuracy as the number of taxa increases.Comment: 32 pages, 5 figures, 1 table
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