I have a set of alleles from sequenced Isolates I want to map to an already existing tree of the same isolates to see which alleles are present in which groups. My problem is I do not know how to map the sequences to the tree and how to properly visualize the resulting Data.
If I understand well your question, you need to map a set "A" of sequences (Your alleles from isolates) to a set "B" of sequences (Which building the already existing tree).
Two configurations:
If you are looking for a FULL-MATCH, it means, you know that you have to find an exact sequence from the set "A" in the set "B". For this, you do not need to use aligners, you can simply do a little script to find the commune sequences between the two sets.
Now, if you are looking for sequences from set "A" with a minimum of 90-95% of identity with sequences from set "B", you have to make alignments. With the Blast standalone program for instance, you can create a database with your set "B", and then align each sequence of the set "A" against this database. You will then have your mapping of each sequence from "A" on "B".
To represent your data, you can add to your tree a symbol for each sequence found. Or an other way, it is with a different color, to write the names of sequences from set "A" found in "B" for each leaf/node which are concerned.
