Generate
Description
Generate a simulated multiple sequence alignment pangraph.
Options
| Name | Type | Short Flag | Long Flag | Description |
|---|---|---|---|---|
| Mutation rate | Float | m | snp-rate | Rate of mutations per site per genome per generation |
| HGT rate | Float | r | hgt-rate | Rate of horizontal transfer events per genome per generation |
| Deletion rate | Float | d | delete-rate | Rate of deletion events per genome per generation |
| Inversion rate | Float | i | invert-rate | Rate of inversion events per genome per generation |
| Graph output | String | o | output-path | Path to location to store simulated pangraph |
| Time | Integer | t | time | Number of generations to simulate before computing sequences and graph |
Arguments
Zero or one fasta file to treat as ancestral sequences. If no file path is given, reads from stdin. In either case, the stream can be optionally gzipped. The number and length of sequences determine the population size.
Output
Outputs all resultant sequences to standard out. Optionally output the resultant pangraph if a path is supplied by the user.