Name
Abstract | ||
|---|---|---|
Phylogenetic reconstruction from gene-order datahas attracted attention from both biologists and computerscientists over the last few years. So far, our softwaresuite GRAPPA is the most accurate approach, but it requiresthat all genomes have identical gene content, witheach gene appearing exactly once in each genome. Someprogress has been made in handling genomes with unequalgene content, both in terms of computing pairwisegenomic distances and in terms of reconstruction.In this paper, we present a new approach for computingthe median of three arbitrary genomes and applyit to the reconstruction of phylogenies from arbitrarygene-order data. We implemented these methodswithin GRAPPAand tested them on simulated datasets undervarious conditions as well as on a real dataset ofchloroplast genomes; we report the results of our simulationsand our analysis of the real dataset and compare themto reconstructions made by using neighbor-joining and usingthe original GRAPPA on the same genomes withequalized gene contents. Our new approach is remarkablyaccurate both in simulations and on the real dataset,in contrast to the distance-based approaches and to reconstructionsusing the original GRAPPAapplied to equalizedgene contents. |
Year | DOI | Venue |
|---|---|---|
2004 | 10.1109/BIBE.2004.1317396 | BIBE |
Keywords | Field | DocType |
arbitrary gene-order data,genomes withequalized gene content,real dataset ofchloroplast genomes,phylogenetic reconstruction,distance-based approach,real dataset,identical gene content,arbitrary genomes,new approach,themto reconstruction,accurate approach,sequences,neighbor joining,computational complexity,phylogeny,bioinformatics,computer science,dna,computational modeling,biology,genetics,genomics | Genome,Neighbor joining,Gene,Computer science,Software suite,Phylogenetic reconstruction,Genomics,Bioinformatics,Phylogenetics,Computational complexity theory | Conference |
ISBN | Citations | PageRank |
0-7695-2173-8 | 19 | 1.20 |
References | Authors | |
11 | 4 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Jijun Tang | 1 | 370 | 48.23 |
| Bernard M. E. Moret | 2 | 1386 | 218.89 |
| Liying Cui | 3 | 44 | 4.28 |
| Claude W. Depamphilis | 4 | 56 | 5.55 |