Sampling species

It is possible that we need to obtain a sample of all the surviving species in our datasets. In that case, we can resort to the script SpeciesSampler to prepare the data. The usage is

python SpeciesSampler Mode ExperimentFolder

This will generate new datasets in which the species that have been not sampled are removed from the output. The modes are:

• i: The user gives a file with the species that must be preserved (one species per line).
• r: The user gives a number between 0 and 1 to determine how many species are randomly sampled
• w: The user gives a file (.tsv) with the name of each lineage in the species tree and the probabilities of sampling that lineage. If the numbers add up to a number over 1, the values are normalized

Samples are created in ./ExperimentFolder/SAMPLES