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- run read.tree command
- rarefy = T/[F]
- freq = 100
- iters - if rarefy
- groups - select specific groups
default - calculate the branch length in a tree (as a fraction of the total number of sequences???) in the tree rarefy=T - perform pd calculation by starting with an empty tree and adding each sequence (based on freq). keep track of pd as a function of sampling effort and produce rarefaction data group - because each tree might represent numerous groups of sequences, the group file will perform calculations for each group separately name - a tree may only represent the unique sequences and the name file would bring in the redundant names