Historian: accurate reconstruction of ancestral sequences and evolutionary rates
نویسندگان
چکیده
منابع مشابه
Historian: accurate reconstruction of ancestral sequences and evolutionary rates
Motivation Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Results Historian combines an efficient reimplementation of the...
متن کاملBranch-and-Bound Reconstruction of Ancestral Sequences
The problem of ancestral sequence reconstruction is the statistical inference of sequences that correspond to internal nodes in a phylgenetic tree [1]. Joint reconstruction is the task of seeking the most likely set of ancestral states corresponding to all the ancestral taxa, while marginal reconstruction aims at inferring the sequence in a specific internal node. In simple probabilistic models...
متن کاملComputational reconstruction of ancestral DNA sequences.
This chapter introduces the problem of ancestral sequence reconstruction: given a set of extant orthologous DNA genomic sequences (or even whole-genomes), together with a phylogenetic tree relating these sequences, predict the DNA sequence of all ancestral species in the tree. Blanchette et al. (1) have shown that for certain sets of species (in particular, for eutherian mammals), very accurate...
متن کاملReconstruction of Ancestral Genomic Sequences Using Likelihood
A challenging task in computational biology is the reconstruction of genomic sequences of extinct ancestors, given the phylogenetic tree and the sequences at the leafs. This task is best solved by calculating the most likely estimate of the ancestral sequences, along with the most likely edge lengths. We deal with this problem and also the variant in which the phylogenetic tree in addition to t...
متن کاملSimple and accurate estimation of ancestral protein sequences.
There are a variety of reasons to reconstruct the sequences of ancient proteins, but whatever the reason, the value of the reconstructed protein depends on the accuracy with which the ancient sequence is inferred. This study uses sequences simulated by a sequence-evolution simulation program that compares parsimony, maximum likelihood, and the Bayesian methods of inferring ancestral sequences a...
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: Bioinformatics
سال: 2017
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btw791