This repository has been archived by the owner on Oct 4, 2018. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathtntlog.run
40 lines (32 loc) · 3.7 KB
/
tntlog.run
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
macro=;
/* To use extended implied weighting, data must be read with implied weights on */
/* Type piwe= into the command line before opening the dataset. */
/* Then if this file is in the same directory as your data file, */
/* type tnt into the TNT command line to run this script. */
xmult:rat10 drift10 hits 15 level 4 chklevel 5;
/* 15 hits gives a quick but less comprehensive run */
outgroup Flustra;
var: nt;
piwe- ;log tnt.rapid.log;xmult;cscores;log/;tsav *TNT/ew.tre;sav;tsav/;nelsen *;set nt ntrees;ttag=;resample=sym replications 100 frequency from 'nt';log TNT/ew.sym;ttag/;log/; keep 0; ttag-; hold 10000;
/* nelsen /L for consensus w/o taxon L */
/*xpiwe=;*/
piwe=3 ;log+ tnt.rapid.log;xmult;cscores;log/;tsav *TNT/xpiwe3.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe3.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=4 ;log+ tnt.rapid.log;xmult;cscores;log/;tsav *TNT/xpiwe4.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe4.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=4.5 ;log+ tnt.rapid.log;xmult;cscores;log/;tsav *TNT/xpiwe4.5.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe4.5.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=5 ;log+ tnt.rapid.log;xmult;cscores;log/;tsav *TNT/xpiwe5.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe5.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=7 ;log+ tnt.rapid.log;xmult;cscores;log/;tsav *TNT/xpiwe7.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe7.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=10.5;log+ tnt.rapid.log;xmult;cscores;log/;tsav *TNT/xpiwe10.5.tre;sav;tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe10.5.sym;ttag/;log/; keep 0; ttag-; hold 10000;
piwe=16 ;log+ tnt.rapid.log;xmult;cscores;log/;tsav *TNT/xpiwe16.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe16.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=24 ;log+ tnt.rapid.log;xmult;cscores;log/;tsav *TNT/xpiwe24.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe24.sym; ttag/;log/; keep 0; ttag-; hold 10000;
/* 1000 hits gives a slow but incredibly comprehensive set of results */
xmult:hits 1000;
piwe- ;log tnt.log;xmult;cscores;log/;tsav *TNT/ew.tre;sav;tsav/;nelsen *;set nt ntrees;ttag=;resample=sym replications 5000 frequency from 'nt';log TNT/ew.sym;ttag/;ttag/;log/; keep 0; ttag-; hold 10000;
/*xpiwe=;*/
piwe=3 ;log+ tnt.log;xmult;cscores;log/;tsav *TNT/xpiwe3.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe3.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=4.5 ;log+ tnt.log;xmult;cscores;log/;tsav *TNT/xpiwe4.5.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe4.5.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=7 ;log+ tnt.log;xmult;cscores;log/;tsav *TNT/xpiwe7.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe7.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=10.5;log+ tnt.log;xmult;cscores;log/;tsav *TNT/xpiwe10.5.tre;sav;tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe10.5.sym;ttag/;log/; keep 0; ttag-; hold 10000;
piwe=16 ;log+ tnt.log;xmult;cscores;log/;tsav *TNT/xpiwe16.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe16.sym; ttag/;log/; keep 0; ttag-; hold 10000;
piwe=24 ;log+ tnt.log;xmult;cscores;log/;tsav *TNT/xpiwe24.tre;sav; tsav/;nelsen *;set nt ntrees;ttag=;resample=frequency from 'nt';log TNT/xpiwe24.sym; ttag/;log/; keep 0; ttag-; hold 10000;
log;
macro -;