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IPPS
2009
IEEE
14 years 1 months ago
Exploring FPGAs for accelerating the phylogenetic likelihood function
Driven by novel biological wet lab techniques such as pyrosequencing there has been an unprecedented molecular data explosion over the last 2-3 years. The growth of biological seq...
Nikolaos Alachiotis, Euripides Sotiriades, Apostol...
BMCBI
2008
86views more  BMCBI 2008»
13 years 7 months ago
Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets
Background: In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogeneti...
Ernesto Picardi, Carla Quagliariello
CSB
2003
IEEE
110views Bioinformatics» more  CSB 2003»
14 years 9 days ago
Prokaryote Phylogeny without Sequence Alignment: From Avoidance Signature to Composition Distance
A new and essentially simple method to reconstruct prokaryotic phylogenetic trees from their complete genome data without using sequence alignment is proposed. It is based on the ...
Bailin Hao, Ji Qi
JCB
2006
124views more  JCB 2006»
13 years 7 months ago
The Average Common Substring Approach to Phylogenomic Reconstruction
We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary. The core of our me...
Igor Ulitsky, David Burstein, Tamir Tuller, Benny ...
ALMOB
2008
85views more  ALMOB 2008»
13 years 7 months ago
Noisy: Identification of problematic columns in multiple sequence alignments
Motivation: Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Larg...
Andreas W. M. Dress, Christoph Flamm, Guido Fritzs...