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ALIFE
2004
14 years 9 months ago
Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods
Phylogenetic trees group organisms by their ancestral relationships. There are a number of distinct algorithms used to reconstruct these trees from molecular sequence data, but dif...
George I. Hagstrom, Dehua H. Hang, Charles Ofria, ...
RECOMB
2009
Springer
15 years 4 months ago
Reconstructing Histories of Complex Gene Clusters on a Phylogeny
Abstract. Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analy...
Tomás Vinar, Brona Brejová, Giltae S...
BMCBI
2008
149views more  BMCBI 2008»
14 years 9 months ago
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence
Background: Modern proteomes evolved by modification of pre-existing ones. It is extremely important to comparative biology that related proteins be identified as members of the s...
Adriano Barbosa-Silva, Venkata P. Satagopam, Reinh...
WABI
2009
Springer
181views Bioinformatics» more  WABI 2009»
15 years 4 months ago
Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes
Abstract. The existing synteny block reconstruction algorithms use anchors (e.g., orthologous genes) shared over all genomes to construct the synteny blocks for multiple genomes. T...
Qian Peng, Max A. Alekseyev, Glenn Tesler, Pavel A...
JACM
2006
99views more  JACM 2006»
14 years 9 months ago
Finding a maximum likelihood tree is hard
Abstract. Maximum likelihood (ML) is an increasingly popular optimality criterion for selecting evolutionary trees [Felsenstein 1981]. Finding optimal ML trees appears to be a very...
Benny Chor, Tamir Tuller