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|clanaa|Clan AA|<div align="justify"> <p>Phylogenetic reconstruction inferred based on clan AA of aspartic peptidases using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As the majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. Several clusters are not supported by this tree, for a better identification of lineages, please see gag-pro-pol tree. </p> <br><p>You can also get a perspective of the ancestral history of this group of enzymes we have reconstructed by maximum likelihood clicking [[ href="phylogeny.php?tree=caard|here ]]. </p> </div>
|chrall|Eukaryotic chromodomains|<div align="justify">Phylogenetic reconstruction inferred based on eukaryotic chromodomains using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|chr|Chromodomains|<div align="justify">Phylogenetic reconstruction inferred based on LTR retroelement chromodomains using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|env_retro|ENV <i>Retroviridae</i> tree|<div align="justify">Phylogenetic reconstruction inferred using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. Several clusters are not supported by this tree, for a better identification of lineages, please see gag-pro-pol tree. </div>
|gag|Gag tree|<div align="justify">Phylogenetic reconstruction inferred based on the LTR retroelement gag capsid-nucleocapsid core using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. Several<em> </em>clusters are not supported by this tree, for a better identification of lineages, please see gag-pro-pol tree. </div>
|gagpol|Gag-pro-pol tree|<div align="justify">Phylogenetic reconstruction inferred based on the concatenated protein product encoded by the gag-pro-pol internal region common to <em>Ty3/Gypsy</em> and <em>Retroviridae</em> LTR retroelements using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|gin|GIN-1 tree|<div align="justify">Phylogenetic reconstruction inferred based on GIN-1 integrases using the parsimony method using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|int|Integrase tree|<div align="justify">Phylogenetic reconstruction inferred based on the LTR retroelemet integrase using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. Several<em> </em>clusters are not supported by this tree, for a better identification of lineages, please see gag-pro-pol tree. </div>
|pr|Protease tree|<div align="justify">Phylogenetic reconstruction inferred based on the LTR retroelemet-like protease using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. Several<em> </em>clusters are not supported by this tree, for a better identification of lineages, please see gag-pro-pol tree. </div>
|pol|Pol tree|<div align="justify">Phylogenetic reconstruction inferred based on the concatenated protein product encoded by the pro-pol internal region common to <em>Ty3/Gypsy</em> and <em>Retroviridae</em> LTR retroelements using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As the majority-rule consensus tree usually consists of all groups that occur more than 50% of the time. We take the consensus values upper of 50 as an equivalent-bootstrapping reference. </div>
|rnaseh|Ribonuclease H tree|<div align="justify">Phylogenetic reconstruction inferred based on the LTR retroelemet-like Ribonuclease H using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. Several<em> </em>clusters are not supported by this tree, for a better identification of lineages, please see gag-pro-pol tree. </div>
|rt|Reverse transcriptase tree|<div align="justify">Phylogenetic reconstruction inferred based on the LTR retroelemet-like reverse transcriptase using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. Several<em> </em>clusters are not supported by this tree, for a better identification of lineages, please see gag-pro-pol tree. </div>
|env_ty3gypsy|ENV <i>Errantiviridae</i> tree|<div align="justify">Phylogenetic reconstruction inferred based on the errantiviridae-like env polyprotein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|dut|dUTPase tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae dUTPase domain using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|nef|NEF tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae nef accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|orfx|ORF-X tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae orf-X accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|rev|REV tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae rev accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. </div>
|rex|REX tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae rex accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As the majority-rule consensus tree usually consists of all groups that occur more than 50% of the time. We take the consensus values upper of 50 as an equivalent-bootstrapping reference. </div>
|sorf|SORF tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae sorf accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|tat|TAT tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae tat accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|tax|TAX tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae tax accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|vif_orfq|VIF_Q tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae vif_orfQ accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference. </div>
|vpr_vpx|VPR_VPX tree|<div align="justify">Phylogenetic reconstruction inferred based on the retroviridae vpr_vpx accessory protein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|env_athila|ENV athila tree|<div align="justify">Phylogenetic reconstruction inferred based on the Athila-like env polyprotein using Felsenstein´s protein sequence parsimony method based on ([[Literature.php?biblioId=684|Eck and Dayhoff 1966)]] and [[Literature.php?biblioId=723|(Fitch 1971)]] to generate a majority-rule consensus tree ([[Literature.php?biblioId=686|Margush and McMorris 1981]]). As majority-rule consensus tree usually consists of all groups that occur more than 50% of the time, we take consensus values upper to 50 as an equivalent-bootstrapping reference.</div>
|caard|Clan AA Reference Database|<div align="justify"><p>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 [[ href="phylogeny.php?tree=clanaa|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.<br /> <br /> </p> <p> 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 ([[Literature.php?biblioId=686|Margush and McMorris 1981]]) inferred using the Felsenstein parsimony method based on the approaches of [[Literature.php?biblioId=684|Eck and Dayhoff (1966)]] and [[Literature.php?biblioId=723|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.</p> </div>
END OF PHYLOTREES

PhylogenyTrees - Revision history

imported>Gydbwiki at 15:24, 26 January 2009