Commands/xmult

From TNT

XMULT
Version: 1.1.
Menu path: to do.

Xmult
Run multiple replications, using sectorial searches, drifting,  ratchet and fusing
combined.  Options are set with "xmult:options;" or "xmult=options;" (using ":" only
settings are changed; "=" runs as well). With "xmult:;" current settings are displayed.
If consensing, / followed by a taxon list removes the specified taxa from the consensus
(this must follow all the other options). If css, rss, and xss are specified css is done first,
then rss, and xss last.

Options are:

     hits N             produce N hits to best length and stop 
     replications N     for each hit, search initially with N replications 
     [no]targetscore N  search until score N found (only with fusing) 
     [no]update         do not update targetscore 
     [no]giveupscore N  give up search as soon as score N found 
     [no]rss            use random sectorial searches (settings with 
                        sectsch:options) 
     [no]css            use constraint sectorial searches (settings with 
                        sectsch:options) 
     [no]xss            use exclusive sectorial searches (settings with 
                        sectsch:options) 
     [no]fuse           use fusing (settings with tfuse:options) 
     [no]gfuse N        every N hits, fuse all trees (=score check) 
     [no]dumpfuse       if fusing fails to produce trees of target score, 
                        dump the trees produced by fusing (may prevent 
                        "clogging" of subsequent fuses by keeping only the 
                        most distinct trees) 
     [no]drift N        use N cycles of drifting (settings with drif:options) 
     [no]ratchet N      use N cycles of ratchet (settings with rat:options) 
     [no]autoconst N    use consensus of previous run and initial stages of 
                        current as constraint for initial stages. 1=previous 
                        and wagner, 2=previous and SPR, 3=previous and TBR.  
                        The first replication of a new hit is never 
                        constrained (i.e. hits are totally independent). 
                        Note that level=2 defaults to 1 when "skipspr" 
                        is on. 
     [no]xmix           after unsuccesful fusing, start a new set of  
                        replications as autoconstrained (otherwise, don't) 
     [no]prvmix         if trees existed in memory before running xmult, use 
                        last one to autoconstrain first xmult replication 
     [no]consense N     consense untill consensus is stabilized N times 
     conbase N          base hits to check for consensus stabilizations 
                        (larger numbers make more reliable estimations) 
     confactor N        factor to increase number of hits to check consensus 
                        stabilization (10-100, larger numbers: more reliable) 
     conmax N           maximum new hits to recheck consensus (default=12) 
     [no]keepall        keep trees from all replications 
     [no]retouch N      before trying new replications, repeat sectorial 
                        search and ratchet/drifting 
     level N            set level of search (0-10). Use 0-2 for easy data 
                        sets, 2-5 for medium, above 5 for difficult 
     chklevel N         check search parameters during run, every N hits. 
                        The parameters are increased or decreased, starting 
                        from user settings.  If N is preceded by +F (between 
                        0 and 2), the entire level is changed by F. If N is 
                        preceded by -, user settings are starting point 
     [no]multiply       after hitting target score, find additional trees 
                        by fusing suboptimal with optimal trees 
     [no]verbose        produce verbose reports

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Example: run an analysis using new technologies.

 TNT will perform random sectorial searches, fuse (2 cycles), drifting (3 cycles) and ratchet (10 cycles) in your search.