... rapidly evolving sites.
... Organize a collection of modern-day sequences according to their evolutionary history
Distance-based methods operate on a table of pairwise distances between sequences
o UPGMA: ~agglomerative clustering; naïve method for tree-building; assumes a molecular clock
(all branches changing at the same ...
Chapter 20 Questions
... Suppose that species 1 and species 3 have similar appearances but very divergent gene
sequences. Species 2 and species 3 have very different appearances but similar gene sequences.
Which pair of species is more likely to be closely related: 1 and 2, or 2 and 3? Explain.
Introduction to Phylogenetics - Lectures For UG-5
... Distance: the other type of data are distance
data, which are computed from DNA or amino
acid sequence data . These data are also called
the distance matrix data, because the distance
are usually presented in the matrix from.
Phylogenetic - Nematode bioinformatics. Analysis tools and data
... Are mathematical and/or statistical methods for inferring the
divergence order of taxa, as well as the lengths of the
branches that connect them. There are many phylogenetic
methods available today, each having strengths and
weaknesses. Most can be classified as follows:
Characters (bp, aa)
... Distance trees were constructed using Neighbor-Joining with a maximum likelihood distance matrix
using the model selected by MODELTEST.
The standard errors of branch lengths were estimated using PAUP .
Divergence dates with low and high confidence intervals and associated evolutionary rates were
Creating Phylogenetic Trees with MEGA
... – At each site, the likelihood is determined by evaluating the
probability that a certain evolutionary model (eg. BLOSSUM or
PAM matrices) has generated the observed data.
– The likelihood’s for each site are then multiplied to provide
likelihood for each tree
– Choose the tree with maximum like ...
... • Phylogenetic analysis is one of the
most controversial areas in
bioinformatics. There are a wide
variety of different methods for
analyzing the data, and even the
experts often disagree on the best
method for analyzing the data.
Phylogenetics Molecular Phylogenetics
... means that it lacks the common ancestor
of (A) the species in the group. Furthermore, a valid taxon that includes the
extant species G, H, J, and K would
necessarily also contain D and E, which
are also descended from A.
Concept Check Questions
... Phylogenetic systematic informs the construction of phylogenetic trees based on shared
A method for paralogy trees reconstruction
... Genes belonging to the same organism are called paralogs when they show a significant similarity
in the sequences, even if they have a different biological function. It is an emergent biological
paradigm that the families of paralogs derive from a mechanism of gene duplication with
modification, rep ...
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms. Traditional phylogenetics relies on morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms, while the more recent field of molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Many forms of molecular phylogenetics are closely related to and make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce the evolutionary tree that represents the historical relationships between the species being analyzed. The historical species tree may also differ from the historical tree of an individual homologous gene shared by those species.Producing a phylogenetic tree requires a measure of homology among the characteristics shared by the taxa being compared. In morphological studies, this requires explicit decisions about which physical characteristics to measure and how to use them to encode distinct states corresponding to the input taxa. In molecular studies, a primary problem is in producing a multiple sequence alignment (MSA) between the genes or amino acid sequences of interest. Progressive sequence alignment methods produce a phylogenetic tree by necessity because they incorporate new sequences into the calculated alignment in order of genetic distance.