From 12829a96afb0d0dba2ea9669e6733d7be86945bf Mon Sep 17 00:00:00 2001 From: Kuoi Date: Wed, 13 Sep 2023 21:05:52 +0800 Subject: [PATCH] polish: update parameters --- README.md | 40 +++++++++++++++++++++++++++++++++------- 1 file changed, 33 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index c8de96a..ab63e59 100644 --- a/README.md +++ b/README.md @@ -12,11 +12,11 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv ## Functions -- Estimate implied weighting K value. +- Extended implied weighting with K value setting (default, default K=12) or implighted weighting with K value setting (default K=12) or equal weighting. -- Search trees via TBR Mult (1000 times) and Xmult (use random sectorial searches, produce 1,000 hits to best length and stop, 10 cycles of drifting, ratchet and fusing). +- Search trees via implicit enumeration (ntax<=25) or TBR Mult (1000 times) (25=75). -- Perform Strict consensus. +- Perform Strict consensus / Majority-rule consensus / Half strict consensus. - Calculate Relative Bremer support, jackknifing (1,000 times), and bootstrap (1,000 times). @@ -26,16 +26,42 @@ The TNT script follows MIT and part of script is from setk.run belonging to Salv ## Options +For Windows users + +``` +tnt run guoyi.run filename datatype weight 0/K cons resample; +``` + +For Linux and Mac users + +``` +tnt run guoyi.run filename datatype weight 0/K cons resample, +``` + +- datatpye should be `32`, `dna`, `prot`, `num` + + - num=number, dna=DNA, prot=protein, 32=max number allowed (default) + +- weight should be `iw`, ew, `eiw` + + - iw=implied weight, ew=equal weight, eiw=extended implied weight (default) N.B. ew must followed 0 (the K value position for ew iw and eiw) + +- cons should be str, mjr, hlf + + - mjr=majority rule, hlf=half, str=strict (default) + +- resample should be sum of what you want + + - jak=1, boot=2, relative bremer=4 i.e. jak+boot+bremer=7 (default) + +## Results + - Results instructions are at the end of `tnt.log`. - `trees.tre`, `resample.tre` are trees with taxname. - `trees_no.tre`, `resample_no.tre` are trees without taxname. -- `nelsen` can be replaced by `majority`. - -- `xmult` and `mult` replications and hold trees number can be adjusted. - - `winclada.tre` can be transferred to the acceptable format for WinClada by tnt2winclada and the output file can be put into Winclada with your tnt matrix file `filename` for mapping apomorphic characters and homoplasy. ## Cite