Phylogenetic analysis of large DNA viruses, especially using methods based on alignment, is often difficult due to the presence of horizontal gene transfer events.
Comparative methods based on alignment folding include RNAalifold (Bernhart et al., 2008; Hofacker et al., 2002) and Pfold (Knudsen and Hein, 2003).
A fast method based on the alignment of diffraction spots perpendicular to interfaces (Δg condition) is proposed, to account for the experimental orientation relationships and interface planes.
Sample HCV core gene sequences were aligned using CLUSTALW and a phylogenetic tree was created using a neighbor-joining method based on the alignment of CP sequences (Kimura 2-parameter model and bootstrap analysis with 1000 replicates), by Molecular Evolutionary Genetics Analysis software version 4.0 (MEGA 4.0).
In addition, we also evaluated the GBDP method based on BLAST alignments (Henz et al. 2005), for which we aligned all pairs of genomes.
The MHC tree was reconstructed with the ML method based on an untrimmed alignment.
Conservation scores were calculated with the PhastCons method based on the multiple alignments of 20 placental mammalian genomes.
The tree was constructed by the neighbor-joining method based on the multiple alignments of the FGF core domains from various organisms.
Also, its comparison against an alignment-based method, based on which almost all conclusions of its superiority were drawn, is inappropriate, as argued above.
Blin et al. [ 13] proposed a greedy method based on algorithms for global alignment that first finds a set of anchors and then recursively match genes found in large common intervals.
In Tohsato et al. (2000), an alignment method based on enzyme hierarchies and enzyme EC number similarity was suggested for the alignment of possibly more than two pathways.
