Title |
Accounting For Alignment Uncertainty in Phylogenomics
|
---|---|
Published in |
PLOS ONE, January 2012
|
DOI | 10.1371/journal.pone.0030288 |
Pubmed ID | |
Authors |
Martin Wu, Sourav Chatterji, Jonathan A. Eisen |
Abstract |
Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy. |
X Demographics
The data shown below were collected from the profiles of 7 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | 43% |
United Kingdom | 1 | 14% |
Cameroon | 1 | 14% |
Unknown | 2 | 29% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 4 | 57% |
Members of the public | 3 | 43% |
Mendeley readers
The data shown below were compiled from readership statistics for 282 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 15 | 5% |
Sweden | 7 | 2% |
United Kingdom | 6 | 2% |
Spain | 5 | 2% |
Germany | 2 | <1% |
Brazil | 2 | <1% |
Australia | 2 | <1% |
Canada | 2 | <1% |
Netherlands | 1 | <1% |
Other | 3 | 1% |
Unknown | 237 | 84% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 80 | 28% |
Researcher | 71 | 25% |
Student > Master | 36 | 13% |
Student > Bachelor | 17 | 6% |
Student > Doctoral Student | 13 | 5% |
Other | 39 | 14% |
Unknown | 26 | 9% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 152 | 54% |
Biochemistry, Genetics and Molecular Biology | 49 | 17% |
Computer Science | 12 | 4% |
Environmental Science | 6 | 2% |
Business, Management and Accounting | 5 | 2% |
Other | 22 | 8% |
Unknown | 36 | 13% |