From 561f88be60a439b7e24ed4c67a42815227024fa3 Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Sat, 5 Apr 2025 18:04:33 +1100
Subject: [PATCH] polish: just add warn to polytomy
---
README.md | 6 ++++--
guoyi.run | 16 ++++++++++------
2 files changed, 14 insertions(+), 8 deletions(-)
diff --git a/README.md b/README.md
index 6dafabf..f715540 100644
--- a/README.md
+++ b/README.md
@@ -52,11 +52,13 @@ tnt run guoyi.run filename datatype weight 0/K cons resample prefix,
- cons should be `str`, `mjr`, `hlf`
- - mjr=majority rule, hlf=half, str=strict (default)
+ - mjr=majority rule, hlf=ea, str=strict (default)
- resample should be sum of what you want
- - relative bremer support (rbrs)=0.1, bremer support (brs)=0.2, jackknifing (jak)=1, bootstrap (boot)=2, symmetric resampling (sym)=4 i.e. rbrs+jak+boot+sym=7.1 (default)
+ - relative bremer support (rbrs)=0.1, bremer support (brs)=0.2, jackknifing (jak)=1, bootstrap (boot)=2, symmetric resampling (sym)=4 i.e. jak+boot+sym=7 (default)
+
+ - Notice: Bremer related support would change the tree topology, so it should be used with caution.
- prefix can be empty or a string
diff --git a/guoyi.run b/guoyi.run
index bd47a27..9bcdd92 100644
--- a/guoyi.run
+++ b/guoyi.run
@@ -111,7 +111,7 @@ end
/*handle resmaple type*/
if (argnumber<6)
- set dojak 1; set doboot 1; set dosym 1; set dorbrs 1;
+ set dojak 1; set doboot 1; set dosym 1; set dorbrs 0;
else
set rsmp %6;
loop 1 5
@@ -356,7 +356,6 @@ set contree ntrees;
/*Store consensus tree to tree vault*/
hold /+0;
tv>/;
-tchoose 0.'npars';
/*Get rbr/br/jak/boot/sym support and get consensus tree*/
ttags=;
@@ -377,18 +376,19 @@ if ('dobremer')
/*calculate relative bremer support*/
if ('dorbrs')
- bs *]!! 0.'npars';
+ bs ]!! 0.'npars';
end
/*calculate bremer support*/
if ('dobrs')
macfloat 1; /*set the br value float*/
- bsupport *!! 0.'npars';
+ bsupport !! 0.'npars';
end
end
-
+
/*Choose final tree*/
+tchoose 0.'npars';
tv<;
tchoose /;
@@ -549,7 +549,11 @@ if ('dohlf')
quote
| half strict consensus tree with |;
end end end
-
+if ('dobremer')
+ quote
+| WARNING: bremer-related will |
+| WARNING: change the polytomy |;
+end
if ('dorbrs')
quote
| relative bremer support |;