Fixed Character States and the Optimization of Molecular Sequence Data

Fixed Character States and the Optimization of Molecular Sequence Data A method is proposed to optimize molecular sequence data that does not employ multiple sequence alignment. This method treats entire homologous contiguous stretches of sequence data as individual characters. This sequence is treated as the homologous unit employed in phylogeny reconstruction. The sets of specific sequences exhibited by the terminal taxa constitute the character states. The number of states is then less than or equal to the number of unique sequences (or homologous fragments) exhibited by the data. A matrix of transformation costs is created to relate the states to one another. The cells of this matrix are defined as the minimum transformation cost between each pair of states based on insertion–deletion and base substitution costs. The diagnosis of a topology then follows existing dynamic programming techniques, with the number of states greatly expanded. Since the possible sequences reconstructed at nodes are limited to those exhibited by the terminals, cladograms constructed in this way may be longer than those of other methods in that they require a greater number of weighted evolutionary events. Example data, the effects of missing data, restricted ancestors, and putative long‐branch attraction are discussed. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Cladistics Wiley

Fixed Character States and the Optimization of Molecular Sequence Data

Cladistics, Volume 15 (4) – Dec 1, 1999

Loading next page...
 
/lp/wiley/fixed-character-states-and-the-optimization-of-molecular-sequence-data-HuIhqCESoS
Publisher
Wiley
Copyright
Copyright © 1999 Wiley Subscription Services, Inc., A Wiley Company
ISSN
0748-3007
eISSN
1096-0031
DOI
10.1111/j.1096-0031.1999.tb00274.x
Publisher site
See Article on Publisher Site

Abstract

A method is proposed to optimize molecular sequence data that does not employ multiple sequence alignment. This method treats entire homologous contiguous stretches of sequence data as individual characters. This sequence is treated as the homologous unit employed in phylogeny reconstruction. The sets of specific sequences exhibited by the terminal taxa constitute the character states. The number of states is then less than or equal to the number of unique sequences (or homologous fragments) exhibited by the data. A matrix of transformation costs is created to relate the states to one another. The cells of this matrix are defined as the minimum transformation cost between each pair of states based on insertion–deletion and base substitution costs. The diagnosis of a topology then follows existing dynamic programming techniques, with the number of states greatly expanded. Since the possible sequences reconstructed at nodes are limited to those exhibited by the terminals, cladograms constructed in this way may be longer than those of other methods in that they require a greater number of weighted evolutionary events. Example data, the effects of missing data, restricted ancestors, and putative long‐branch attraction are discussed.

Journal

CladisticsWiley

Published: Dec 1, 1999

You’re reading a free preview. Subscribe to read the entire article.


DeepDyve is your
personal research library

It’s your single place to instantly
discover and read the research
that matters to you.

Enjoy affordable access to
over 18 million articles from more than
15,000 peer-reviewed journals.

All for just $49/month

Explore the DeepDyve Library

Search

Query the DeepDyve database, plus search all of PubMed and Google Scholar seamlessly

Organize

Save any article or search result from DeepDyve, PubMed, and Google Scholar... all in one place.

Access

Get unlimited, online access to over 18 million full-text articles from more than 15,000 scientific journals.

Your journals are on DeepDyve

Read from thousands of the leading scholarly journals from SpringerNature, Wiley-Blackwell, Oxford University Press and more.

All the latest content is available, no embargo periods.

See the journals in your area

DeepDyve

Freelancer

DeepDyve

Pro

Price

FREE

$49/month
$360/year

Save searches from
Google Scholar,
PubMed

Create folders to
organize your research

Export folders, citations

Read DeepDyve articles

Abstract access only

Unlimited access to over
18 million full-text articles

Print

20 pages / month

PDF Discount

20% off