Access the full text.
Sign up today, get DeepDyve free for 14 days.
(1997)
POY: The Optimization bility of random similarity should decrease to marof Alignment Characters. Program and Documentation. New York. ginal levels
ple DNA sequences are routinely determined for phy
P. Goloboff (1993)
CHARACTER OPTIMIZATION AND CALCULATION OF TREE LENGTHSCladistics, 9
This fixed-character-state method
W. Wheeler (1995)
SEQUENCE ALIGNMENT, PARAMETER SENSITIVITY, AND THE PHYLOGENETIC ANALYSIS OF MOLECULAR DATASystematic Biology, 44
(1998)
The phylogeny of the chelicerate orders
W. Wheeler (1996)
OPTIMIZATION ALIGNMENT: THE END OF MULTIPLE SEQUENCE ALIGNMENT IN PHYLOGENETICS?Cladistics, 12
(1998)
sequence string itself, this method offers a certain sim-Goloboff
P. Goloboff (1998)
Tree Searches Under Sankoff ParsimonyCladistics, 14
K. Nixon, Jerrold Davis (1991)
POLYMORPHIC TAXA, MISSING VALUES AND CLADISTIC ANALYSISCladistics, 7
D. Sankoff, P. Rousseau (1975)
Locating the vertices of a steiner tree in an arbitrary metric spaceMathematical Programming, 9
(1997)
POY: The Optimization of Alignment Characters
Sagl Needle, Asd Christus, D. Wuksch
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
D. Sankoff, P. Rousseau (1975)
Locating the vertices of a Steiner tree in arbitrary spaceMathematical Programming, 9
As we gather more data, the proba
(1991)
On missing tionships. As sequencing technology improves, multientries in cladistic analysis
N. Platnick, C. Griswold, J. Coddington (1991)
ON MISSING ENTRIES IN CLADISTIC ANALYSISCladistics, 7
Q. Wheeler (1990)
ONTOGENY AND CHARACTER PHYLOGENYCladistics, 6
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.
Cladistics – Wiley
Published: Dec 1, 1999
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.