Ancestral sequence reconstruction for co-evolutionary models
نویسندگان
چکیده
Abstract The ancestral sequence reconstruction problem is the inference, back in time, of properties common ancestors from measured contemporary populations. Standard algorithms for this assume independent (factorized) evolution characters sequences, which generally wrong (e.g. proteins and genome sequences). In work, we have studied sequences described by global co-evolutionary models, reproduce pattern cooperative interactions between elements that compose it. For this, first modeled temporal correlated real valued a multivariate Ornstein–Uhlenbeck process on finite tree. This represents as Gaussian vectors evolving quadratic potential, who describe selection forces acting entities. Under Bayesian framework, developed algorithm these obtained an analytical expression to quantify quality our estimation. We extend formalism discrete applying method Potts model. showed both continuous configurations, there wide range parameters where, properly reconstruct intra-species correlations must be taken into account. also demonstrated that, with elements, outperforms traditional schemes based site approximations.
منابع مشابه
Ancestral sequence reconstruction with phangorn
For parsimony analysis of the edge length represent the observed number of changes. Reconstructiong ancestral states therefore defines also the edge lengths of a tree. However there can exist several equally parsimonious reconstructions or states can be ambiguous and therefore edge length can differ. ”MPR” reconstructs the ancestral states for each (internal) node as if the tree would be rooted...
متن کاملAncestral Sequence Reconstruction with Maximum Parsimony.
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first reconstruct a phylogenetic tree with some tree inference method and then to use some method of ancestral state inference based on that tree. One of the best-know...
متن کاملAncestral sequence reconstruction with phangorn (Version 2.2.0)
For parsimony analysis of the edge length represent the observed number of changes. Reconstructing ancestral states therefore defines also the edge lengths of a tree. However there can exist several equally parsimonious reconstructions or states can be ambiguous and therefore edge length can differ. ”MPR” reconstructs the ancestral states for each (internal) node as if the tree would be rooted ...
متن کاملAncestral sequence reconstruction with phangorn (Version 2.0.0)
For parsimony analysis of the edge length represent the observed number of changes. Reconstructing ancestral states therefore defines also the edge lengths of a tree. However there can exist several equally parsimonious reconstructions or states can be ambiguous and therefore edge length can differ. ”MPR” reconstructs the ancestral states for each (internal) node as if the tree would be rooted ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Statistical Mechanics: Theory and Experiment
سال: 2022
ISSN: ['1742-5468']
DOI: https://doi.org/10.1088/1742-5468/ac3d93