FAQ
FAQ
1. What is FaSe?
FaSe is short for Fake Sequencer, simulating molecular evolution by mutating nucleic acid or protein sequences to a user specified percent divergence.
2. What is "Divergence Percentage"?
The divergence percentage determines the mutation count in the most mutated sequence in a generation. It refers to the length of the sequence, meaning a 10% divergence will allow up to 10% of the sequence to be mutated.
3. What is "Maximum Children Per Parent"?
The maximum children determine the upper bound on how many sequences can be created from a parent sequence (chosen randomly for each parent between zero and this upper bound).
4. What is “Generation Type”?
The generation type essentially determines the method of how the sequences generated will be related to each other.
Sequence Mutator
“Sequence Mutator” runs a single lineage of mutations, a single parent, and outputs it in a FASTA-like list format. The mutations compound from the previous sequence, all the way up until the divergence percentage is met.
If the maximum number of children is less than the number of mutations, the remaining ones will be compounded into the final sequence.
For example, if it is 0.5, the number of mutations that occur in the most mutated sequence will be equal to half the length of the sequence. Keep in mind that mutations may overwrite previous mutations, so even if the divergence percentage is 1.0 it does not necessarily mean the entire sequence will be mutated.
Phylogenetic Tree
“Phylogenetic Tree” acts similarly except that each mutated sequence from the original sequence will also have its own children, allowing for there to be up to 4 generations including the original. The divergence percentage will compound on the previously mutated sequence.