I'm using pxbp version 1.3 and the command pxbp -t rs_test_rr.trees -o rs_test.txt. Trees are rooted.
The output (full output attached) has OUTGROUP repeated multiple times in a clade. Additionally, OUTGROUP OUTGROUP is repeated on multiple lines but with different counts.
I was getting similar results with my full dataset so I have attached a simplified subset of trees and the output.
I'm using pxbp version 1.3 and the command pxbp -t rs_test_rr.trees -o rs_test.txt. Trees are rooted.
The output (full output attached) has OUTGROUP repeated multiple times in a clade. Additionally, OUTGROUP OUTGROUP is repeated on multiple lines but with different counts.
I was getting similar results with my full dataset so I have attached a simplified subset of trees and the output.
100 trees 419 unique clades found CLADE: OUTGROUP OUTGROUP FREQ: 0.220472 ICA: -0.353365 COUNT: 28 TREEFREQ: 0.28 CLADE: OUTGROUP OUTGROUP OUTGROUP FREQ: 0.525926 ICA: 0.382861 COUNT: 71 TREEFREQ: 0.71 CLADE: Sp_H OUTGROUP OUTGROUP FREQ: 0.338542 ICA: 0.248714 COUNT: 65 TREEFREQ: 0.65 CLADE: OUTGROUP Sp_O FREQ: 0.932692 ICA: 0.812806 COUNT: 97 TREEFREQ: 0.97 CLADE: Sp_H Sp_C Sp_A OUTGROUP OUTGROUP FREQ: 0.0132626 ICA: -0.122379 COUNT: 5 TREEFREQ: 0.05 CLADE: FREQ: 0.0289256 ICA: -0.365935 COUNT: 7 TREEFREQ: 0.07 CLADE: Sp_I Sp_K Sp_O FREQ: 0.0227273 ICA: -0.282593 COUNT: 5 TREEFREQ: 0.05 CLADE: Sp_I Sp_K Sp_O Sp_N FREQ: 0.00413223 ICA: -0.220597 COUNT: 2 TREEFREQ: 0.02 CLADE: OUTGROUP OUTGROUP FREQ: 0.00995025 ICA: -0.207823 COUNT: 6 TREEFREQ: 0.06 CLADE: Sp_I Sp_O Sp_N Sp_M Sp_H Sp_C FREQ: 0.00330579 ICA: -0.120959 COUNT: 2 TREEFREQ: 0.02
pxbp_test.zip