Phylogeny:AP CAARD (clan AA Reference DB)

AP clan AA aspartic peptidasesAP Bel/PaoAP CaulimoviridaeAP Caulimoviridae dom2AP LTR retroelementsAP RetroviridaeAP Ty1/CopiaAP Ty3/GypsyATF CaulimovirusBel1 SpumaretrovirusBel2 SpumaretrovirusCHR Ty1/CopiaCHR eukaryote protein domainsCHR retroelementCOAT CaulimoviridaeCOATPOL CaulimoviridaeENV Athila (Ty3/Gypsy)ENV Errantiviridae (Ty3/Gypsy)ENV RetroviridaeENV Sire (Ty1/Copia)GAG Bel/PaoGAG RetroviridaeGAG Ty1/CopiaGAG Ty3/GypsyGAGPOL Bel/PaoGAGPOL RetroviridaeGAGPOL Ty1/CopiaGAGPOL Ty3/GypsyGPYF LTR retroelementsINT Bel/PaoINT GIN/GINGERINT LTR retroelementsINT RetroviridaeINT Ty1/CopiaINT Ty3/GypsyMOV CaulimoviridaeNEF LentiviridaeORF2 BadnavirusORFB SoymovirusORFC SoymovirusORFX BetaretrovirusPOL Bel/PaoPOL CaulimoviridaePOL LTR retroelementsPOL RetroviridaePOL Ty1/CopiaPOL Ty3/GypsyREV LentivirusREX LentivirusRNaseH Bel/PaoRNaseH CaulimoviridaeRNaseH LTR retroelementsRNaseH RetroviridaeRNaseH Ty1/CopiaRNaseH Ty3/GypsyRT Bel/PaoRT CaulimoviridaeRT LTR retroelementsRT RetroviridaeRT Ty1/CopiaRT Ty3/GypsySORF BetaretrovirusTAT LentivirusTAV CaulimoviridaeTAX DeltaretrovirusVAP CaulimoviridaeVIF-Q LentivirusVPR-VPX LentivirusdUTPase retroelements

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Method of phylogenenetic reconstruction

The Clan AA Reference Database (CAARD), an in-progress database of ancestral maximum likelihood reconstructions (AMLRs), sequence logos and HMMs constructed based on different protein families according to estimations of their taxonomy and relationships. The objetive is to investigate the major consensus and phylogeny to classify the different protein families. The current version is based on 323 non-redundant sequences belonging to different clan AA families (to visualize a conventional phylogeny inferred based on these sequences, click here). The set of tools is stored by family datasheets in the database, which can be navigated using the phylogenetic tree shown in this web site. This tree acts as dynamic map of links. By clicking the name of each cluster in this tree, the user can locate the datasheet corresponding to the family selected.

The tree has been reconstructed based on an alignment of AMLR sequences available clicking on the blue circle in the center of the tree. Additionally, the sequences can be retrieved in 2 independent ways, one) within each data sheet as a Jrof alignment, 2) leaves link to the AMLR sequences which are available in separate files. Sequences have tags with information about the parental relationships of the sequence represented by each leaf. "N_x" means the ancestral ML sequence (or node) reconstructed per ancestral reconstruction. The topology is a MRC tree (Margush and McMorris 1981) inferred using the Felsenstein parsimony method based on the approaches of Eck and Dayhoff (1966) and Fitch (1971). Values accompanying the clusters are two independent bootstrap estimations (separated by bars) supporting clusters that occurred >55% of the time in the analysis when using the parsimony and NJ methods of phylogenetic reconstruction, respectively. Branches are not distance-scaled.

Citation

Llorens,C. Futami,R., Renaud,G and A. Moya (2009). Bioinformatic Flowchart and Database to Investigate the Origins and Diversity of Clan AA Peptidases. Biology Direct, 4:3.