gethmmtree

Retrieve phylogenetic tree data from PFAM database

Syntax

Tree = gethmmtree(PFAMName)
Tree = gethmmtree(PFAMAccessionNumber)
Tree = gethmmtree(PFAMNumber)

Tree = gethmmtree(...'ToFile', ToFileValue, ...)
Tree = gethmmtree(...'Type', TypeValue, ...)

Input Arguments

PFAMNameString specifying a protein family name (unique identifier) of an HMM profile record in the PFAM database. For example, '7tm_2'.
PFAMAccessionNumberString specifying a protein family accession number of an HMM profile record in the PFAM database. For example, 'PF00002'.
PFAMNumberInteger specifying a protein family number of an HMM profile record in the PFAM database. For example, 2 is the protein family number for the protein family PF0002.
ToFileValueProperty to specify the location and file name for saving data. Enter either a file name or a path and file name supported by your system (ASCII text file).
TypeValueString that specifies which alignments to include in the tree. Choices are:
  • 'seed' — Returns a tree with only the alignments used to generate the HMM model.

  • 'full' (default) — Returns a tree with all of the alignments that match the model.

    Warning   Setting the 'Type' name-value pair argument to 'seed' or 'full' is now ignored since the PFAM database no longer provides trees for the full alignment. This name-value pair argument will be removed in a future release. To download the 'seed' tree use gethmmtree without any extra input arguments. To obtain the 'full' tree you may use the gethmmalignment function to download the 'full' alignment and build a tree using the seqpdist and seqneighjoin functions as illustrated in the following example.

Output Arguments

TreeAn object containing a phylogenetic tree representative of the protein family.

Description

Tree = gethmmtree(PFAMName) searches the PFAM database for the record represented by PFAMName, a protein family name, retrieves information, and returns Tree, an object containing a phylogenetic tree representative of the protein family.

Tree = gethmmtree(PFAMAccessionNumber) searches the PFAM database for the record represented by PFAMAccessionNumber, a protein family accession number, retrieves information, and returns Tree, an object containing a phylogenetic tree representative of the protein family.

Tree = gethmmtree(PFAMNumber) determines a protein family accession number from PFAMNumber, an integer, searches the PFAM database for the associated record, retrieves information, and returns Tree, an object containing a phylogenetic tree representative of the protein family.

Tree = gethmmtree(...'PropertyName', PropertyValue, ...) calls gethmmtree with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:


Tree = gethmmtree(...'ToFile', ToFileValue, ...)
saves the data returned from the PFAM database in the file ToFileValue.

Tree = gethmmtree(...'Type', TypeValue, ...) specifies which alignments to include in the tree. Choices for TypeValue are:

  • 'seed' — Returns a tree with only the alignments used to generate the HMM model.

  • 'full' (default) — Returns a tree with all of the alignments that match the model.

    Warning   Setting the 'Type' name-value pair argument to 'seed' or 'full' is now ignored since the PFAM database no longer provides trees for the full alignment. This name-value pair argument will be removed in a future release. To download the 'seed' tree use gethmmtree without any extra input arguments. To obtain the 'full' tree you may use the gethmmalignment function to download the 'full' alignment and build a tree using the seqpdist and seqneighjoin functions as illustrated in the following example.

Examples

Retrieve phylogenetic tree built from the multiple-aligned sequences used to train the HMM profile model for global alignment. The PFAM accession number PF00002 is for the 7-transmembrane receptor protein in the secretin family.

tree  = gethmmtree('PF00002');

Recover the 'full' tree for the same family by downloading the full multiple sequence alignment and building the tree using the seqdist and seqneighjoin functions. It may take some considerable amount of time to calculate the tree for large families.

seqs = gethmmalignment('PF00002','type','full');
dis = seqpdist(seqs);
tree = seqneighjoin(dis,'equivar',seqs);
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