First you will need to compile rind on your computer.
Then you need to create a script called "treescript", that rind will execute to make a tree from the distance file. See the rind.doc file for more information. Another method is to simply put what you think is the correct unrooted tree in the file "treefile" in nested-parentheses format (this is required when using the -u or -U options.
Then you must put your alignment (preferably an amino acid alignment using the one-letter representation; but DNA or RNA will also work) in a file called "data". The sequences can be interleaved or not, but the sequence names must all be different, and must be 10 characters long (these may include blank spaces at the end).
Then type "rind". After execution, the best tree rind was able to make is in the file "besttree"; "counts" shows the expected number of times each residue was used in the tree in each position; "entropy" gives the entropy of each position; and "model" gives full details of the best site-specific model.
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