Phylogenetic analyses of alignments with gaps
نویسندگان
چکیده
Background
منابع مشابه
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic ...
متن کاملMaximum Likelihood Phylogenetic Inference is Consistent on Multiple Sequence Alignments, with or without Gaps
We prove that maximum likelihood phylogenetic inference is consistent on gapped multiple sequence alignments (MSAs) as long as substitution rates across each edge are greater than zero, under mild assumptions on the structure of the alignment. Under these assumptions, maximum likelihood will asymptotically recover the tree with edge lengths corresponding to the mean number of substitutions per ...
متن کاملMeasuring guide-tree dependency of inferred gaps in progressive aligners
MOTIVATION Multiple sequence alignments are generally reconstructed using a progressive approach that follows a guide-tree. During this process, gaps are introduced at a cost to maximize residue pairing, but it is unclear whether inferred gaps reflect actual past events of sequence insertions or deletions. It has been found that patterns of inferred gaps in alignments contain information toward...
متن کاملParsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an ali...
متن کاملOptimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns
MOTIVATION Multiple sequence alignments (MSAs) are widely used approaches in bioinformatics to carry out other tasks such as structure predictions, biological function analyses or phylogenetic modeling. However, current tools usually provide partially optimal alignments, as each one is focused on specific biological features. Thus, the same set of sequences can produce different alignments, abo...
متن کامل