Computational protocol: Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses

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Protocol publication

[…] Virus sequences were edited using BioEdit Sequence Alignment Editor (Hall, 1999) and SeqEdit (DNAStar, Madison, WI) to obtain a consensus sequence for each. Reference geminiviruses for full length CP and CR sequence alignments were compiled by extracting the complete DNA-A and DNA-B sequences, the CP ORF (approximately 765–777 bp) and CR sequences (approximately 150–170 bp) from sequences available in GenBank (accession # are provided in the figures). Multiple sequence alignments of the full-length DNA-A, DNA-B, capsid protein (CP) gene and common region (CR) were carried out using the Clustal Program (MegAlign, DNAStar). The phylogenetic trees were constructed from the multiple alignments by the neighbor-joining majority rule consensus. Multiple alignments were analyzed by maximum parsimony with full-length DNA-A, DNA-B and CP phylogenetic trees using Phylogenetic Analysis Using Parsimony (PAUP) [] and a bootstrap analysis with 1000 replicates was performed. Only values above 50% were reported on the trees in the figures. Virus specific iterons in the CR of selected CMGs were identified and compared with the analogous iterons of the Tanzanian isolates of CMGs. […]

Pipeline specifications

Software tools BioEdit, PAUP*
Application Phylogenetics
Organisms Manihot esculenta, East African cassava mosaic Cameroon virus, East African cassava mosaic virus, African cassava mosaic virus