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Protocol publication

[…] The obtained original sequences were assembled with ContigExpress (VectorNTI Suite 8.0; Invitrogen, USA) and aligned with HCV reference sequences using Bioedit and ClustalX. Alignment was manually adjusted to maximize alignment and minimize gaps. Clear sequence information for 591nt of 5′NCR/C region, 921nt of the C/E2 region, and 884nt of NS5B region was selected for genotyping and phylogenetic analysis. HCV genotypes were assigned following the phylogenetic analysis, in which the sequences were compared with reference sequences from the HCV database located in Loa Alamos (http://hcv.lanl.gov/content/sequence/HCV/ToolsOutline.html). The tree construction procedure was performed in PAUP* version 4.0b10. All characters were equally weighted, and gaps were treated as missing data. Trees were inferred using the heuristic search option with tree bisection-reconnection (TBR) branch swapping and 1,000 random sequence additions. Max-trees were set to 5,000, branches of zero length were collapsed, and all parsimonious trees were saved. The reliability of trees was tested by non-parametric bootstrapping in 1,000 replications. Cluster bootstrap values above 70% were considered as significant . Descriptive tree statistics, including tree length (TL), consistency index (CI), retention index (RI), rescaled consistency index (RC) and homoplasy index (HI), were calculated for each obtained MPT. […]

Pipeline specifications

Software tools Vector NTI Advance, BioEdit, Clustal W, PAUP*
Organisms Classical swine fever virus, Homo sapiens
Diseases Hepatitis, Hepatitis C, Immunologic Deficiency Syndromes, Infection, Wiskott-Aldrich Syndrome, HIV Infections, Coinfection