Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment.

نویسندگان

  • K Strimmer
  • A von Haeseler
چکیده

We introduce a graphical method, likelihood-mapping, to visualize the phylogenetic content of a set of aligned sequences. The method is based on an analysis of the maximum likelihoods for the three fully resolved tree topologies that can be computed for four sequences. The three likelihoods are represented as one point inside an equilateral triangle. The triangle is partitioned in different regions. One region represents star-like evolution, three regions represent a well-resolved phylogeny, and three regions reflect the situation where it is difficult to distinguish between two of the three trees. The location of the likelihoods in the triangle defines the mode of sequence evolution. If n sequences are analyzed, then the likelihoods for each subset of four sequences are mapped onto the triangle. The resulting distribution of points shows whether the data are suitable for a phylogenetic reconstruction or not.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Maximum-likelihood analysis using TREE-PUZZLE.

TREE-PUZZLE provides a means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e., groups of four sequences. Basic Protocol 1 explains how to reconstruct trees based on the maximum-likelihood principle and quartet puzzling. Basic Protocol 2 discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. Basic Protocol...

متن کامل

An Evolutionary and Phylogenetic Study of the BMP15 Gene

DNA sequence data contains a wealth of biologically useful information. Recent innovations in DNA sequencing technology have greatly increased our capacity to determine massive amounts of nucleotide sequences. These sequences can be used to specify the characteristics of different regions, interpret the evolutionary relationships between categorized groups, likelihood of performing multiple com...

متن کامل

Genetic Characterization of Argas persicus From Iran by Sequencing of Mitochondrial Cytochrome Oxidase I (COX1) and 16s rRNA Genes

Background: Argas persicus has a great importance for health and veterinary, it can transmit many infectious agents such as Borrelia anserina (avian spirochetosis) and Aegyptianella pullorum. Distinguishing Argasidae due to close morphological relationship is difficult. OBJECTIVES: In the present study, we performed molecular analyses based on PCR and sequencing of Amplicon derived from 16S rRN...

متن کامل

Maximum 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 کامل

Analysis of genetic diversity, phylogenetic relationships and population structure of Arasbaran cornelian cherry (Cornus mas L.) genotypes using ISSR molecular markers

Cornelian cherry (Cornus mas L.), considered as the ancestor of cultivated trees in Arasbaran region, is a medicinally and economically plant species. However, little is known about genetic diversity, breeding programs, and population structure of this species in mentioned region. Keeping this in view, the main objectives of present study were to analysis the genetic diversity, phyloge...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Proceedings of the National Academy of Sciences of the United States of America

دوره 94 13  شماره 

صفحات  -

تاریخ انتشار 1997