SUMMARY The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion and deletion history and finally inferring substitutions. Each of these steps have received lot of attention in the past years. However, there currently exists no fr...

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, reprodu...

The accurate reconstruction of phylogenies from short molecular sequences is an important problem in computational biology. Recent work has highlighted deep connections between sequence-length requirements for highprobability phylogeny reconstruction and the related problem of the estimation of ancestral sequences. In [Daskalakis et al.’09], building on the work of [Mossel’04], a tight sequence...

The accurate reconstruction of phylogenies from short molecular sequences is an important problem in computational biology. Recent work has highlighted deep connections between sequence-length requirements for high-probability phylogeny reconstruction and the related problem of the estimation of ancestral sequences. In Daskalakis et al. (in Probab. Theory Relat. Fields 2010), building on the wo...

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a ...

We consider the problem of inferring an ancestral state from observations at leaves a tree, assuming evolves along tree according to two-state symmetric Markov process. establish general branching rate condition under which maximum parsimony, common reconstruction method requiring only knowledge topology (but not substitution rates or other parameters), succeeds better than random guessing unif...

Inferences about the evolution of continuous traits based on reconstruction of ancestral states have often been considered more error-prone than analysis of independent contrasts. Here we show that both methods in fact yield identical estimators for the correlation coefficient and regression gradient of correlated traits, indicating that reconstructed ancestral states are a valid source of info...

Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also being compared and contrasted in order to identify other functional sequences, such as those involved in the regulation of genes. In cases where DNA sequences f...

Supplemental
Section
S1
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Genome
Sequencing
and
Assembly........................................... 2
 Supplemental
Section
S2
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Indel
Assessment
With
the
Neutral
Indel
Model ................11
 Supplemental
Section
S3
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Great
Ape
Divergence
Estimate
via
WGS
Read
Mapping..11
 Supplemental
Section
S4
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Short
Read
Sequencing................................................................13
 Suppl...