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Issue 13: Bremer support does not seem to work in build2398
2 people starred this issue and may be notified of changes. Back to list
Status:  Accepted
Owner:  ----
Type-Enhancement
Priority-Medium
Milestone-Release4.1


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Reported by psimm...@lamar.colostate.edu, Nov 02, 2007 
What steps will reproduce the problem?

read ("eq97.fas")
set (root: "Seq1")
transform ((all, tcm:(1,1)), gap_opening:1)
build (branch_and_bound, trees:100)
calculate_support (bremer, build(100), swap(trees:100))
report ("eq97.bremer", supports)
report (supports)

What is the expected output? 

Bremer support of 3 for the clade of (Seq3, Seq4)

What do you see instead?

Bremer Supports:
Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]Support tree:
(Seq1 (Seq2 (Seq3 Seq4)[1.#INF])[1.#INF])[1.#INF]


What version of the product are you using? On what operating system?

ncurses_poy.exe build2398 on Windows

Please provide any additional information below.
Comment 1 by avaron, Nov 05, 2007 
(No comment was entered for this change.)
Status: Accepted
Labels: -Priority-Medium Priority-High
Comment 2 by avaron, Nov 05, 2007 
Thanks for the feedback.

Can you verify that the result is correct if you use swap (all) as the swap option for calculate_support? as in:

calculate_support (bremer, build(100), swap(trees:100, all))

My suspicion is that an improved heuristic is not letting the swapper evaluate the suboptimal trees.
Comment 3 by psimm...@lamar.colostate.edu, Nov 05, 2007 
Thanks, Andres.  Yep, that works correctly for me too.  I got: 

(Seq1 (Seq2 (Seq3 Seq4)[3.])[1.#INF])[1.#INF]Support tree:

, albeit repeated 100 times.  I trust the 100x repitition in the support file is a 
minor bug in release 2398 of POY rather than there being 100 separate most 
parsimonious trees, each with a Bremer support of 3.  

I'll use the "all" addition in all of my future jackknife/bootstrap/Bremer support 
scripts.  I noticed that the "all" fix only applied to Bremer support in release 
2398 though.

Mark
Comment 4 by avaron, Nov 06, 2007 
The 100 trees occur because there are 100 trees in memory. POY is reporting support values for each one of 
them. You might want to add a select () statement between the build and calculate_support commands.
Comment 5 by psimm...@lamar.colostate.edu, Nov 06, 2007 
Thanks, Andres.  Quite right that I had taken the select() command out and should 
have added it back in.

Mark
Comment 6 by avaron, Nov 10, 2007 
The feature is not really a bug. After discussing it internally, we have decided not to weaken the heuristics for a 
problem that will be rather limited for real datasets. But new options will be added in the future to let the user 
tune a little better than talking either build (all) or build ().
Labels: -Type-Defect -Priority-High Type-Enhancement Priority-Medium
Comment 7 by avaron, Feb 25, 2008 
(No comment was entered for this change.)
Labels: Milestone-Release4.1
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