guided placement of two queries to the same node

[W M]

Is it possible to do guided placement and direct multiple queries to the same node? If so, how should this be indicated in NHX format?

[Ari Loytynoja]

Hello,

Sorry for the delay in answering your question.

It is possible to direct any number of sequences to the same node; it is also possible to direct sequences to several nodes from which PAGAN then finds the best-matching node separately for each sequence and, after the assignment, aligns each sequence to the node that that particular sequence matches the best. Currently PAGAN supports only one tag for each node and each sequence and all sequences with the same tag are handles in a similar manner.

An example of this is shown in http://code.google.com/p/pagan-msa/wiki/PAGAN?tm=6#Example_of_guided_placement_of_protein_sequences. If you look at the example data file at http://code.google.com/p/pagan-msa/source/browse/examples/protein_placement/input_aa_frags.fas, you can see that the sequences have either the tag TID=01 ("Primate") or TID=02 ("Rodent"); the reference tree has (http://code.google.com/p/pagan-msa/source/browse/examples/protein_placement/reference_tree.nhx) has tagged five nodes, two with TID=01 and three with TID=02, and all the sequences will be placed to these nodes. (The tagged nodes are indicated with yellow dots in the tree http://wiki.pagan-msa.googlecode.com/git/images/guide_tree.png.)

Best regards, Ari

On 05/07/2013 11:54 PM, W M wrote:

Is it possible to do guided placement and direct multiple queries to the
same node? If so, how should this be indicated in NHX format?

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