Returns a connector to a phylomeDB3 database.
db: database name in the host server. host: hostname in which phylomeDB is hosted. user: username to the database. port: port used to connect database. passwd: password to connect database.
An object whose methods can be used to query the database.
Returns how many alignments are for a given phylome
Retuns the frequency of each evolutionary method in the input phylome
Return the either the clean, the raw or both alignments for the input phylomeDB ID in the input phylome
Returns all the isoforms registered for the input phylomeDB ID
Returns information about which methods have been used to reconstruct every tree for a given phylomeDB ID grouped by phylome
return a tree for input id in the given phylome for the best fitting evolutionary model in terms of LK
Return the raw alignment for the input phylomeDB ID in the given phylome
Return the trees where the protid is presented as part of the homolog sequences to the seed protein
Returns all the external IDs registered in the ‘external_id’ table that are associated to the input phylomeDB IDs
Returns the phylomeDB IDs for a given genome in the database filtering out, or not, the different isoforms for each ID
Returns all available information about a registered genome/proteome
Returns all current available genomes/proteomes
Return all the proteomes/genomes registered for the input taxaid code
Returns all available GO Terms associated to the input phylomeDB IDs
Returns the protein id associated to a given external id
Returns all the registered translations of a given phylomeDB ID
Return all the available information for a given set of homologous sequences extracted from a tree from a given phylome.
Returns the longest isoform for a given phylomeDB ID
Return the conversion between an old phylomeDB ID and a new one
Returns all old phylomeDB IDs associated to each of the input phylomeDB IDs
Returns all alignments available for a given phylome
Returns available information on a given phylome
Returns the seed phylomeDB IDs for a given phylome being possible to filter out the longest isoforms
Returns all trees available for a given phylome
Returns all current available phylomes
Given a list of phylomeDB IDs, return in which phylomes these IDs have been used as a seed
Returns all possible protein and gene names associated to the input phylomeDB IDs
Returns a list of proteomes associated to a given phylome_id
Return the raw alignment for the input phylomeDB ID in the given phylome
Return all the available information for each sequence from tree/s asociated to a tuple (protein, phylome) identifiers.
Return all available information for the homologous sequences to the input phylomeDB ID in the input phylome using the best tree to compute the set of homologous sequences
Returns available information about a given protid
Returns all sequences of a given proteome, filtering the
Returns all current registered species in the database
Returns a list of proteomes associated to a given phylome_id
Returns all information on a given species/code
Depending in the input parameters select either .- a tree with the best evolutionary model in terms of LK (best_tree) .- a tree reconstructed using a specific model (method) .- all available model/trees for the tuple (phylomeDB ID, phylome ID)
Returns a list of the longest isoforms for each proteome where the ID is already registered. The ID can be a current phylomeDB ID version, former phylomeDB ID or an external ID.