phame.ctl

       refdir = /users  # directory where reference files are located
      workdir = /users  # directory where contigs/reads files are located and output is stored

    reference = 1  # 0:pick a random reference; 1:use given reference
      reffile = Ecoli.fna  # reference filename 

      project = snp_alignment  # project name, output files will have project name as suffix

      cdsSNPS = 0  # 0:no cds SNPS; 1:cds SNPs

    FirstTime = 1  # 1:yes; 2:update existing SNP alignment

         data = 0  # 0:only complete(F); 1:only contig(C); 2:only reads(R); 
                   # 3:combination F+C; 4:combination F+R; 5:combination C+R; 
                   # 6:combination F+C+R; 7:realignment  *See below 
        reads = 2  # 1: single reads; 2: paired reads; 3: both types present;

         tree = 0  # 0:no tree; 1:use FastTree; 2:use RAxML; 3:use both;
    modelTest = 0  # 0:no; 1:yes;  # Only used when building a tree using RAxML
    bootstrap = 0  # 0:no; 1:yes;  # Run bootstrapping  *See below
            N = 100  # Number of bootstraps to run *See below    
 
    PosSelect = 2  # 0:No; 1:use PAML; 2:use HyPhy; 3:use both *See below

         code = 0  # 0:Bacteria; 1:Virus; 2:Eukaryote

        clean = 0  # 0:no clean; 1:clean

      threads = 1  # Number of threads to use

       cutoff = 0  # Mismatch cutoff - ignore SNPs within cutoff length of each other.

* When using data option 1,2,5 need a complete reference to align/map to. 
* Use data option 7 when need to extract SNPs using a sublist of already aligned genomes. 

* Bootstrapping is run on tree produced by RAxML. 
* Bootstrapping is only run on Fastatree when RAxML option is turned off.
* Default number of bootstraps is based on RAxML default. 

* PosSelect default = 0 (no molecular evolutionary analysis is run). 
* HyPhy option when running molecular evolutionary analysis is recommended.