guoyi.run: TNT Script for Maximum Parsimony Analysis

Extended implied weighting with K value setting (default, default K=12) or implied weighting with K value setting (default K=12) or equal weighting.

Search trees via implicit enumeration (ntax<=25, but not for eiw) or TBR Mult (1000 times) with branch swapping (25<ntax<75, also for ntax<=25 with eiw) or Mult with branch swapping and Xmult (use random sectorial searches, produce 50 hits to best length and stop, 10 cycles of drifting, ratchet and fusing) (ntax>=75).

Perform Strict consensus / Majority-rule consensus (without bremer support variations) / Half strict consensus (without bremer support variations).

Calculate relative Bremer support, bremer support, jackknifing (1,000 times), bootstrap (1,000 times) and symmetric resampling (1,000 times).

Map apomorphic characters on the consensus tree.

Calculate Tree lenght (TL), Consistency Index (CI) and Retention Index (RI).

Generate ss file which can be read by Winclada directly.