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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
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A Practical Guide to Phylogenetics for Nonexperts
12:00

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Published on: February 5, 2014

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.

Ari Löytynoja1, Nick Goldman

  • 1EMBL-European Bioinformatics Institute, Hinxton, Cambridgeshire, UK. ari@ebi.ac.uk

BMC Bioinformatics
|November 30, 2010
PubMed
Summary
This summary is machine-generated.

webPRANK is a new web server that simplifies phylogeny-aware multiple sequence alignment. It offers an intuitive interface for aligning DNA, protein, and codon sequences, aiding evolutionary analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogeny-aware progressive alignment, implemented in PRANK, excels in phylogenetic alignment benchmarks and aids in inferring selection on codon sequences.
  • PRANK's advanced features, including modeling complex evolutionary processes and inferring posterior probabilities, can be challenging for users to optimize and interpret.
  • Users often face difficulties in generating optimal alignments, visualizing comprehensive results, and post-processing, such as selecting alignment sites based on reliability.

Purpose of the Study:

  • To develop a user-friendly web server, webPRANK, that provides easy access to the PRANK phylogeny-aware alignment algorithm.
  • To simplify the process of generating, visualizing, and post-processing multiple sequence alignments.
  • To make advanced phylogeny-aware alignment accessible to a broader user base through a web interface.

Main Methods:

  • Developed webPRANK, a web server integrating the PRANK phylogeny-aware alignment algorithm.
  • Implemented support for DNA, protein, and codon sequence alignment, including protein-translated cDNA alignment and genomic sequence alignment with built-in structure models.
  • Created a web-based alignment browser for visualizing results in the context of a cladogram, facilitating post-processing tasks like removing unreliable alignment columns.

Main Results:

  • The webPRANK server offers an easy-to-use interface for phylogeny-aware multiple sequence alignment.
  • Supports diverse sequence types (DNA, protein, codon, cDNA) and includes features for genomic sequence alignment.
  • Provides a powerful alignment browser for visualization and post-processing, enabling selective removal of low-reliability alignment columns.
  • Facilitates inference of ancestral sequences with realistic gap patterns and annotation of existing alignments.

Conclusions:

  • webPRANK integrates phylogeny-aware multiple sequence alignment, visualization, and post-processing into a single, user-friendly web interface.
  • Expands accessibility to advanced multiple sequence alignment techniques for a wider range of researchers.
  • Enables comprehensive alignment-related activities for small-scale projects using only a standard web browser.