parsimony!

Commands in mothur
1

Hello,

I did the parsimony command and the resulting output was as follows:

"mothur > parsimony(tree=final.bacteria.an.thetayc.0.03.ave.tre, group=lakeextractnames.design, groups=all)


Using 1 processors. ********************#****#****#****#****#****#****#****#****#****#****# Comparing to random:|||||||||||||||||||||||||||||||||||||||||||||||||||| *********************************************************************** Tree# Groups ParsScore ParsSig 1 ArL-DNA-F-ArL-cDNA-F 1 1

1 ArL-DNA-F-LA-DNA-S 1 1

1 ArL-cDNA-F-LA-DNA-S 1 1

1 ArL-DNA-F-LA-cDNA-S 1 1

1 ArL-cDNA-F-LA-cDNA-S 1 1

1 LA-DNA-S-LA-cDNA-S 1 1

1 ArL-DNA-F-LL-DNA-F 1 1

1 ArL-cDNA-F-LL-DNA-F 1 1

1 LA-DNA-S-LL-DNA-F 1 1

1 LA-cDNA-S-LL-DNA-F 1 1

1 ArL-DNA-F-LL-cDNA-F 1 1

1 ArL-cDNA-F-LL-cDNA-F 1 1

1 LA-DNA-S-LL-cDNA-F 1 1

1 LA-cDNA-S-LL-cDNA-F 1 1

1 LL-DNA-F-LL-cDNA-F 1 1

1 ArL-DNA-F-ML-DNA-S 1 1

1 ArL-cDNA-F-ML-DNA-S 1 1

1 LA-DNA-S-ML-DNA-S 1 1

1 LA-cDNA-S-ML-DNA-S 1 1

1 LL-DNA-F-ML-DNA-S 1 1

1 LL-cDNA-F-ML-DNA-S 1 1

1 ArL-DNA-F-ML-cDNA-S 1 1

1 ArL-cDNA-F-ML-cDNA-S 1 1

1 LA-DNA-S-ML-cDNA-S 1 1

1 LA-cDNA-S-ML-cDNA-S 1 1

1 LL-DNA-F-ML-cDNA-S 1 1

1 LL-cDNA-F-ML-cDNA-S 1 1

1 ML-DNA-S-ML-cDNA-S 1 1

1 ArL-DNA-F-MR-DNA-F 1 1

1 ArL-cDNA-F-MR-DNA-F 1 1

1 LA-DNA-S-MR-DNA-F 1 1

1 LA-cDNA-S-MR-DNA-F 1 1

1 LL-DNA-F-MR-DNA-F 1 1

1 LL-cDNA-F-MR-DNA-F 1 1

1 ML-DNA-S-MR-DNA-F 1 1

1 ML-cDNA-S-MR-DNA-F 1 1

1 ArL-DNA-F-MR-cDNA-F 1 1

1 ArL-cDNA-F-MR-cDNA-F 1 1

1 LA-DNA-S-MR-cDNA-F 1 1

1 LA-cDNA-S-MR-cDNA-F 1 1

1 LL-DNA-F-MR-cDNA-F 1 1

1 LL-cDNA-F-MR-cDNA-F 1 1

1 ML-DNA-S-MR-cDNA-F 1 1

1 ML-cDNA-S-MR-cDNA-F 1 1

1 MR-DNA-F-MR-cDNA-F 1 1

1 ArL-DNA-F-NGSL-DNA-S 1 1

1 ArL-cDNA-F-NGSL-DNA-S 1 1

1 LA-DNA-S-NGSL-DNA-S 1 1

1 LA-cDNA-S-NGSL-DNA-S 1 1

1 LL-DNA-F-NGSL-DNA-S 1 1

1 LL-cDNA-F-NGSL-DNA-S 1 1

1 ML-DNA-S-NGSL-DNA-S 1 1

1 ML-cDNA-S-NGSL-DNA-S 1 1

1 MR-DNA-F-NGSL-DNA-S 1 1

1 MR-cDNA-F-NGSL-DNA-S 1 1

1 ArL-DNA-F-NGSLfall-DNA-S 1 1

1 ArL-cDNA-F-NGSLfall-DNA-S 1 1

1 LA-DNA-S-NGSLfall-DNA-S 1 1

1 LA-cDNA-S-NGSLfall-DNA-S 1 1

1 LL-DNA-F-NGSLfall-DNA-S 1 1

1 LL-cDNA-F-NGSLfall-DNA-S 1 1

1 ML-DNA-S-NGSLfall-DNA-S 1 1

1 ML-cDNA-S-NGSLfall-DNA-S 1 1

1 MR-DNA-F-NGSLfall-DNA-S 1 1

1 MR-cDNA-F-NGSLfall-DNA-S 1 1

1 NGSL-DNA-S-NGSLfall-DNA-S 1 1

1 ArL-DNA-F-NGSLspr-DNA-S 1 1

1 ArL-cDNA-F-NGSLspr-DNA-S 1 1

1 LA-DNA-S-NGSLspr-DNA-S 1 1

1 LA-cDNA-S-NGSLspr-DNA-S 1 1

1 LL-DNA-F-NGSLspr-DNA-S 1 1

1 LL-cDNA-F-NGSLspr-DNA-S 1 1

1 ML-DNA-S-NGSLspr-DNA-S 1 1

1 ML-cDNA-S-NGSLspr-DNA-S 1 1

1 MR-DNA-F-NGSLspr-DNA-S 1 1

1 MR-cDNA-F-NGSLspr-DNA-S 1 1

1 NGSL-DNA-S-NGSLspr-DNA-S 1 1

1 NGSLfall-DNA-S-NGSLspr-DNA-S 1 1

1 ArL-DNA-F-NGSLsum-DNA-S 1 1

1 ArL-cDNA-F-NGSLsum-DNA-S 1 1

1 LA-DNA-S-NGSLsum-DNA-S 1 1

1 LA-cDNA-S-NGSLsum-DNA-S 1 1

1 LL-DNA-F-NGSLsum-DNA-S 1 1

1 LL-cDNA-F-NGSLsum-DNA-S 1 1

1 ML-DNA-S-NGSLsum-DNA-S 1 1

1 ML-cDNA-S-NGSLsum-DNA-S 1 1

1 MR-DNA-F-NGSLsum-DNA-S 1 1

1 MR-cDNA-F-NGSLsum-DNA-S 1 1

1 NGSL-DNA-S-NGSLsum-DNA-S 1 1

1 NGSLfall-DNA-S-NGSLsum-DNA-S 1 1

1 NGSLspr-DNA-S-NGSLsum-DNA-S 1 1

1 ArL-DNA-F-PO-DNA-S 1 1

1 ArL-cDNA-F-PO-DNA-S 1 1

1 LA-DNA-S-PO-DNA-S 1 1

1 LA-cDNA-S-PO-DNA-S 1 1

1 LL-DNA-F-PO-DNA-S 1 1

1 LL-cDNA-F-PO-DNA-S 1 1

1 ML-DNA-S-PO-DNA-S 1 1

1 ML-cDNA-S-PO-DNA-S 1 1

1 MR-DNA-F-PO-DNA-S 1 1

1 MR-cDNA-F-PO-DNA-S 1 1

1 NGSL-DNA-S-PO-DNA-S 1 1

1 NGSLfall-DNA-S-PO-DNA-S 1 1

1 NGSLspr-DNA-S-PO-DNA-S 1 1

1 NGSLsum-DNA-S-PO-DNA-S 1 1

1 ArL-DNA-F-PO-cDNA-S 1 1

1 ArL-cDNA-F-PO-cDNA-S 1 1

1 LA-DNA-S-PO-cDNA-S 1 1

1 LA-cDNA-S-PO-cDNA-S 1 1

1 LL-DNA-F-PO-cDNA-S 1 1

1 LL-cDNA-F-PO-cDNA-S 1 1

1 ML-DNA-S-PO-cDNA-S 1 1

1 ML-cDNA-S-PO-cDNA-S 1 1

1 MR-DNA-F-PO-cDNA-S 1 1

1 MR-cDNA-F-PO-cDNA-S 1 1

1 NGSL-DNA-S-PO-cDNA-S 1 1

1 NGSLfall-DNA-S-PO-cDNA-S 1 1

1 NGSLspr-DNA-S-PO-cDNA-S 1 1

1 NGSLsum-DNA-S-PO-cDNA-S 1 1

1 PO-DNA-S-PO-cDNA-S 1 1

1 ArL-DNA-F-RL-DNA-F 1 1

1 ArL-cDNA-F-RL-DNA-F 1 1

1 LA-DNA-S-RL-DNA-F 1 1

1 LA-cDNA-S-RL-DNA-F 1 1

1 LL-DNA-F-RL-DNA-F 1 1

1 LL-cDNA-F-RL-DNA-F 1 1

1 ML-DNA-S-RL-DNA-F 1 1

1 ML-cDNA-S-RL-DNA-F 1 1

1 MR-DNA-F-RL-DNA-F 1 1

1 MR-cDNA-F-RL-DNA-F 1 1

1 NGSL-DNA-S-RL-DNA-F 1 1

1 NGSLfall-DNA-S-RL-DNA-F 1 1

1 NGSLspr-DNA-S-RL-DNA-F 1 1

1 NGSLsum-DNA-S-RL-DNA-F 1 1

1 PO-DNA-S-RL-DNA-F 1 1

1 PO-cDNA-S-RL-DNA-F 1 1

1 ArL-DNA-F-SGSL-DNA-S 1 1

1 ArL-cDNA-F-SGSL-DNA-S 1 1

1 LA-DNA-S-SGSL-DNA-S 1 1

1 LA-cDNA-S-SGSL-DNA-S 1 1

1 LL-DNA-F-SGSL-DNA-S 1 1

1 LL-cDNA-F-SGSL-DNA-S 1 1

1 ML-DNA-S-SGSL-DNA-S 1 1

1 ML-cDNA-S-SGSL-DNA-S 1 1

1 MR-DNA-F-SGSL-DNA-S 1 1

1 MR-cDNA-F-SGSL-DNA-S 1 1

1 NGSL-DNA-S-SGSL-DNA-S 1 1

1 NGSLfall-DNA-S-SGSL-DNA-S 1 1

1 NGSLspr-DNA-S-SGSL-DNA-S 1 1

1 NGSLsum-DNA-S-SGSL-DNA-S 1 1

1 PO-DNA-S-SGSL-DNA-S 1 1

1 PO-cDNA-S-SGSL-DNA-S 1 1

1 RL-DNA-F-SGSL-DNA-S 1 1

1 ArL-DNA-F-SGSL-cDNA-S 1 1

1 ArL-cDNA-F-SGSL-cDNA-S 1 1

1 LA-DNA-S-SGSL-cDNA-S 1 1

1 LA-cDNA-S-SGSL-cDNA-S 1 1

1 LL-DNA-F-SGSL-cDNA-S 1 1

1 LL-cDNA-F-SGSL-cDNA-S 1 1

1 ML-DNA-S-SGSL-cDNA-S 1 1

1 ML-cDNA-S-SGSL-cDNA-S 1 1

1 MR-DNA-F-SGSL-cDNA-S 1 1

1 MR-cDNA-F-SGSL-cDNA-S 1 1

1 NGSL-DNA-S-SGSL-cDNA-S 1 1

1 NGSLfall-DNA-S-SGSL-cDNA-S 1 1

1 NGSLspr-DNA-S-SGSL-cDNA-S 1 1

1 NGSLsum-DNA-S-SGSL-cDNA-S 1 1

1 PO-DNA-S-SGSL-cDNA-S 1 1

1 PO-cDNA-S-SGSL-cDNA-S 1 1

1 RL-DNA-F-SGSL-cDNA-S 1 1

1 SGSL-DNA-S-SGSL-cDNA-S 1 1

1 ArL-DNA-F-SGSLfall-DNA-S 1 1

1 ArL-cDNA-F-SGSLfall-DNA-S 1 1

1 LA-DNA-S-SGSLfall-DNA-S 1 1

1 LA-cDNA-S-SGSLfall-DNA-S 1 1

1 LL-DNA-F-SGSLfall-DNA-S 1 1

1 LL-cDNA-F-SGSLfall-DNA-S 1 1

1 ML-DNA-S-SGSLfall-DNA-S 1 1

1 ML-cDNA-S-SGSLfall-DNA-S 1 1

1 MR-DNA-F-SGSLfall-DNA-S 1 1

1 MR-cDNA-F-SGSLfall-DNA-S 1 1

1 NGSL-DNA-S-SGSLfall-DNA-S 1 1

1 NGSLfall-DNA-S-SGSLfall-DNA-S 1 1

1 NGSLspr-DNA-S-SGSLfall-DNA-S 1 1

1 NGSLsum-DNA-S-SGSLfall-DNA-S 1 1

1 PO-DNA-S-SGSLfall-DNA-S 1 1

1 PO-cDNA-S-SGSLfall-DNA-S 1 1

1 RL-DNA-F-SGSLfall-DNA-S 1 1

1 SGSL-DNA-S-SGSLfall-DNA-S 1 1

1 SGSL-cDNA-S-SGSLfall-DNA-S 1 1

1 ArL-DNA-F-SGSLfall-cDNA-S 1 1

1 ArL-cDNA-F-SGSLfall-cDNA-S 1 1

1 LA-DNA-S-SGSLfall-cDNA-S 1 1

1 LA-cDNA-S-SGSLfall-cDNA-S 1 1

1 LL-DNA-F-SGSLfall-cDNA-S 1 1

1 LL-cDNA-F-SGSLfall-cDNA-S 1 1

1 ML-DNA-S-SGSLfall-cDNA-S 1 1

1 ML-cDNA-S-SGSLfall-cDNA-S 1 1

1 MR-DNA-F-SGSLfall-cDNA-S 1 1

1 MR-cDNA-F-SGSLfall-cDNA-S 1 1

1 NGSL-DNA-S-SGSLfall-cDNA-S 1 1

1 NGSLfall-DNA-S-SGSLfall-cDNA-S 1 1

1 NGSLspr-DNA-S-SGSLfall-cDNA-S 1 1

1 NGSLsum-DNA-S-SGSLfall-cDNA-S 1 1

1 PO-DNA-S-SGSLfall-cDNA-S 1 1

1 PO-cDNA-S-SGSLfall-cDNA-S 1 1

1 RL-DNA-F-SGSLfall-cDNA-S 1 1

1 SGSL-DNA-S-SGSLfall-cDNA-S 1 1

1 SGSL-cDNA-S-SGSLfall-cDNA-S 1 1

1 SGSLfall-DNA-S-SGSLfall-cDNA-S 1 1

1 ArL-DNA-F-SGSLspr-DNA-S 1 1

1 ArL-cDNA-F-SGSLspr-DNA-S 1 1

1 LA-DNA-S-SGSLspr-DNA-S 1 1

1 LA-cDNA-S-SGSLspr-DNA-S 1 1

1 LL-DNA-F-SGSLspr-DNA-S 1 1

1 LL-cDNA-F-SGSLspr-DNA-S 1 1

1 ML-DNA-S-SGSLspr-DNA-S 1 1

1 ML-cDNA-S-SGSLspr-DNA-S 1 1

1 MR-DNA-F-SGSLspr-DNA-S 1 1

1 MR-cDNA-F-SGSLspr-DNA-S 1 1

1 NGSL-DNA-S-SGSLspr-DNA-S 1 1

1 NGSLfall-DNA-S-SGSLspr-DNA-S 1 1

1 NGSLspr-DNA-S-SGSLspr-DNA-S 1 1

1 NGSLsum-DNA-S-SGSLspr-DNA-S 1 1

1 PO-DNA-S-SGSLspr-DNA-S 1 1

1 PO-cDNA-S-SGSLspr-DNA-S 1 1

1 RL-DNA-F-SGSLspr-DNA-S 1 1

1 SGSL-DNA-S-SGSLspr-DNA-S 1 1

1 SGSL-cDNA-S-SGSLspr-DNA-S 1 1

1 SGSLfall-DNA-S-SGSLspr-DNA-S 1 1

1 SGSLfall-cDNA-S-SGSLspr-DNA-S 1 1

1 ArL-DNA-F-SGSLspr-cDNA-S 1 1

1 ArL-cDNA-F-SGSLspr-cDNA-S 1 1

1 LA-DNA-S-SGSLspr-cDNA-S 1 1

1 LA-cDNA-S-SGSLspr-cDNA-S 1 1

1 LL-DNA-F-SGSLspr-cDNA-S 1 1

1 LL-cDNA-F-SGSLspr-cDNA-S 1 1

1 ML-DNA-S-SGSLspr-cDNA-S 1 1

1 ML-cDNA-S-SGSLspr-cDNA-S 1 1

1 MR-DNA-F-SGSLspr-cDNA-S 1 1

1 MR-cDNA-F-SGSLspr-cDNA-S 1 1

1 NGSL-DNA-S-SGSLspr-cDNA-S 1 1

1 NGSLfall-DNA-S-SGSLspr-cDNA-S 1 1

1 NGSLspr-DNA-S-SGSLspr-cDNA-S 1 1

1 NGSLsum-DNA-S-SGSLspr-cDNA-S 1 1

1 PO-DNA-S-SGSLspr-cDNA-S 1 1

1 PO-cDNA-S-SGSLspr-cDNA-S 1 1

1 RL-DNA-F-SGSLspr-cDNA-S 1 1

1 SGSL-DNA-S-SGSLspr-cDNA-S 1 1

1 SGSL-cDNA-S-SGSLspr-cDNA-S 1 1

1 SGSLfall-DNA-S-SGSLspr-cDNA-S 1 1

1 SGSLfall-cDNA-S-SGSLspr-cDNA-S 1 1

1 SGSLspr-DNA-S-SGSLspr-cDNA-S 1 1

1 ArL-DNA-F-SGSLsum-DNA-S 1 1

1 ArL-cDNA-F-SGSLsum-DNA-S 1 1

1 LA-DNA-S-SGSLsum-DNA-S 1 1

1 LA-cDNA-S-SGSLsum-DNA-S 1 1

1 LL-DNA-F-SGSLsum-DNA-S 1 1

1 LL-cDNA-F-SGSLsum-DNA-S 1 1

1 ML-DNA-S-SGSLsum-DNA-S 1 1

1 ML-cDNA-S-SGSLsum-DNA-S 1 1

1 MR-DNA-F-SGSLsum-DNA-S 1 1

1 MR-cDNA-F-SGSLsum-DNA-S 1 1

1 NGSL-DNA-S-SGSLsum-DNA-S 1 1

1 NGSLfall-DNA-S-SGSLsum-DNA-S 1 1

1 NGSLspr-DNA-S-SGSLsum-DNA-S 1 1

1 NGSLsum-DNA-S-SGSLsum-DNA-S 1 1

1 PO-DNA-S-SGSLsum-DNA-S 1 1

1 PO-cDNA-S-SGSLsum-DNA-S 1 1

1 RL-DNA-F-SGSLsum-DNA-S 1 1

1 SGSL-DNA-S-SGSLsum-DNA-S 1 1

1 SGSL-cDNA-S-SGSLsum-DNA-S 1 1

1 SGSLfall-DNA-S-SGSLsum-DNA-S 1 1

1 SGSLfall-cDNA-S-SGSLsum-DNA-S 1 1

1 SGSLspr-DNA-S-SGSLsum-DNA-S 1 1

1 SGSLspr-cDNA-S-SGSLsum-DNA-S 1 1

1 ArL-DNA-F-SGSLsum-cDNA-S 1 1

1 ArL-cDNA-F-SGSLsum-cDNA-S 1 1

1 LA-DNA-S-SGSLsum-cDNA-S 1 1

1 LA-cDNA-S-SGSLsum-cDNA-S 1 1

1 LL-DNA-F-SGSLsum-cDNA-S 1 1

1 LL-cDNA-F-SGSLsum-cDNA-S 1 1

1 ML-DNA-S-SGSLsum-cDNA-S 1 1

1 ML-cDNA-S-SGSLsum-cDNA-S 1 1

1 MR-DNA-F-SGSLsum-cDNA-S 1 1

1 MR-cDNA-F-SGSLsum-cDNA-S 1 1

1 NGSL-DNA-S-SGSLsum-cDNA-S 1 1

1 NGSLfall-DNA-S-SGSLsum-cDNA-S 1 1

1 NGSLspr-DNA-S-SGSLsum-cDNA-S 1 1

1 NGSLsum-DNA-S-SGSLsum-cDNA-S 1 1

1 PO-DNA-S-SGSLsum-cDNA-S 1 1

1 PO-cDNA-S-SGSLsum-cDNA-S 1 1

1 RL-DNA-F-SGSLsum-cDNA-S 1 1

1 SGSL-DNA-S-SGSLsum-cDNA-S 1 1

1 SGSL-cDNA-S-SGSLsum-cDNA-S 1 1

1 SGSLfall-DNA-S-SGSLsum-cDNA-S 1 1

1 SGSLfall-cDNA-S-SGSLsum-cDNA-S 1 1

1 SGSLspr-DNA-S-SGSLsum-cDNA-S 1 1

1 SGSLspr-cDNA-S-SGSLsum-cDNA-S 1 1

1 SGSLsum-DNA-S-SGSLsum-cDNA-S 1 1

1 ArL-DNA-F-SS-DNA-S 1 1

1 ArL-cDNA-F-SS-DNA-S 1 1

1 LA-DNA-S-SS-DNA-S 1 1

1 LA-cDNA-S-SS-DNA-S 1 1

1 LL-DNA-F-SS-DNA-S 1 1

1 LL-cDNA-F-SS-DNA-S 1 1

1 ML-DNA-S-SS-DNA-S 1 1

1 ML-cDNA-S-SS-DNA-S 1 1

1 MR-DNA-F-SS-DNA-S 1 1

1 MR-cDNA-F-SS-DNA-S 1 1

1 NGSL-DNA-S-SS-DNA-S 1 1

1 NGSLfall-DNA-S-SS-DNA-S 1 1

1 NGSLspr-DNA-S-SS-DNA-S 1 1

1 NGSLsum-DNA-S-SS-DNA-S 1 1

1 PO-DNA-S-SS-DNA-S 1 1

1 PO-cDNA-S-SS-DNA-S 1 1

1 RL-DNA-F-SS-DNA-S 1 1

1 SGSL-DNA-S-SS-DNA-S 1 1

1 SGSL-cDNA-S-SS-DNA-S 1 1

1 SGSLfall-DNA-S-SS-DNA-S 1 1

1 SGSLfall-cDNA-S-SS-DNA-S 1 1

1 SGSLspr-DNA-S-SS-DNA-S 1 1

1 SGSLspr-cDNA-S-SS-DNA-S 1 1

1 SGSLsum-DNA-S-SS-DNA-S 1 1

1 SGSLsum-cDNA-S-SS-DNA-S 1 1

1 ArL-DNA-F-SS-cDNA-S 1 1

1 ArL-cDNA-F-SS-cDNA-S 1 1

1 LA-DNA-S-SS-cDNA-S 1 1

1 LA-cDNA-S-SS-cDNA-S 1 1

1 LL-DNA-F-SS-cDNA-S 1 1

1 LL-cDNA-F-SS-cDNA-S 1 1

1 ML-DNA-S-SS-cDNA-S 1 1

1 ML-cDNA-S-SS-cDNA-S 1 1

1 MR-DNA-F-SS-cDNA-S 1 1

1 MR-cDNA-F-SS-cDNA-S 1 1

1 NGSL-DNA-S-SS-cDNA-S 1 1

1 NGSLfall-DNA-S-SS-cDNA-S 1 1

1 NGSLspr-DNA-S-SS-cDNA-S 1 1

1 NGSLsum-DNA-S-SS-cDNA-S 1 1

1 PO-DNA-S-SS-cDNA-S 1 1

1 PO-cDNA-S-SS-cDNA-S 1 1

1 RL-DNA-F-SS-cDNA-S 1 1

1 SGSL-DNA-S-SS-cDNA-S 1 1

1 SGSL-cDNA-S-SS-cDNA-S 1 1

1 SGSLfall-DNA-S-SS-cDNA-S 1 1

1 SGSLfall-cDNA-S-SS-cDNA-S 1 1

1 SGSLspr-DNA-S-SS-cDNA-S 1 1

1 SGSLspr-cDNA-S-SS-cDNA-S 1 1

1 SGSLsum-DNA-S-SS-cDNA-S 1 1

1 SGSLsum-cDNA-S-SS-cDNA-S 1 1

1 SS-DNA-S-SS-cDNA-S 1 1

1 ArL-DNA-F-SWL-DNA-F 1 1

1 ArL-cDNA-F-SWL-DNA-F 1 1

1 LA-DNA-S-SWL-DNA-F 1 1

1 LA-cDNA-S-SWL-DNA-F 1 1

1 LL-DNA-F-SWL-DNA-F 1 1

1 LL-cDNA-F-SWL-DNA-F 1 1

1 ML-DNA-S-SWL-DNA-F 1 1

1 ML-cDNA-S-SWL-DNA-F 1 1

1 MR-DNA-F-SWL-DNA-F 1 1

1 MR-cDNA-F-SWL-DNA-F 1 1

1 NGSL-DNA-S-SWL-DNA-F 1 1

1 NGSLfall-DNA-S-SWL-DNA-F 1 1

1 NGSLspr-DNA-S-SWL-DNA-F 1 1

1 NGSLsum-DNA-S-SWL-DNA-F 1 1

1 PO-DNA-S-SWL-DNA-F 1 1

1 PO-cDNA-S-SWL-DNA-F 1 1

1 RL-DNA-F-SWL-DNA-F 1 1

1 SGSL-DNA-S-SWL-DNA-F 1 1

1 SGSL-cDNA-S-SWL-DNA-F 1 1

1 SGSLfall-DNA-S-SWL-DNA-F 1 1

1 SGSLfall-cDNA-S-SWL-DNA-F 1 1

1 SGSLspr-DNA-S-SWL-DNA-F 1 1

1 SGSLspr-cDNA-S-SWL-DNA-F 1 1

1 SGSLsum-DNA-S-SWL-DNA-F 1 1

1 SGSLsum-cDNA-S-SWL-DNA-F 1 1

1 SS-DNA-S-SWL-DNA-F 1 1

1 SS-cDNA-S-SWL-DNA-F 1 1

1 ArL-DNA-F-SWL-cDNA-F 1 1

1 ArL-cDNA-F-SWL-cDNA-F 1 1

1 LA-DNA-S-SWL-cDNA-F 1 1

1 LA-cDNA-S-SWL-cDNA-F 1 1

1 LL-DNA-F-SWL-cDNA-F 1 1

1 LL-cDNA-F-SWL-cDNA-F 1 1

1 ML-DNA-S-SWL-cDNA-F 1 1

1 ML-cDNA-S-SWL-cDNA-F 1 1

1 MR-DNA-F-SWL-cDNA-F 1 1

1 MR-cDNA-F-SWL-cDNA-F 1 1

1 NGSL-DNA-S-SWL-cDNA-F 1 1

1 NGSLfall-DNA-S-SWL-cDNA-F 1 1

1 NGSLspr-DNA-S-SWL-cDNA-F 1 1

1 NGSLsum-DNA-S-SWL-cDNA-F 1 1

1 PO-DNA-S-SWL-cDNA-F 1 1

1 PO-cDNA-S-SWL-cDNA-F 1 1

1 RL-DNA-F-SWL-cDNA-F 1 1

1 SGSL-DNA-S-SWL-cDNA-F 1 1

1 SGSL-cDNA-S-SWL-cDNA-F 1 1

1 SGSLfall-DNA-S-SWL-cDNA-F 1 1

1 SGSLfall-cDNA-S-SWL-cDNA-F 1 1

1 SGSLspr-DNA-S-SWL-cDNA-F 1 1

1 SGSLspr-cDNA-S-SWL-cDNA-F 1 1

1 SGSLsum-DNA-S-SWL-cDNA-F 1 1

1 SGSLsum-cDNA-S-SWL-cDNA-F 1 1

1 SS-DNA-S-SWL-cDNA-F 1 1

1 SS-cDNA-S-SWL-cDNA-F 1 1

1 SWL-DNA-F-SWL-cDNA-F 1 1

1 ArL-DNA-F-UL-DNA-F 1 1

1 ArL-cDNA-F-UL-DNA-F 1 1

1 LA-DNA-S-UL-DNA-F 1 1

1 LA-cDNA-S-UL-DNA-F 1 1

1 LL-DNA-F-UL-DNA-F 1 1

1 LL-cDNA-F-UL-DNA-F 1 1

1 ML-DNA-S-UL-DNA-F 1 1

1 ML-cDNA-S-UL-DNA-F 1 1

1 MR-DNA-F-UL-DNA-F 1 1

1 MR-cDNA-F-UL-DNA-F 1 1

1 NGSL-DNA-S-UL-DNA-F 1 1

1 NGSLfall-DNA-S-UL-DNA-F 1 1

1 NGSLspr-DNA-S-UL-DNA-F 1 1

1 NGSLsum-DNA-S-UL-DNA-F 1 1

1 PO-DNA-S-UL-DNA-F 1 1

1 PO-cDNA-S-UL-DNA-F 1 1

1 RL-DNA-F-UL-DNA-F 1 1

1 SGSL-DNA-S-UL-DNA-F 1 1

1 SGSL-cDNA-S-UL-DNA-F 1 1

1 SGSLfall-DNA-S-UL-DNA-F 1 1

1 SGSLfall-cDNA-S-UL-DNA-F 1 1

1 SGSLspr-DNA-S-UL-DNA-F 1 1

1 SGSLspr-cDNA-S-UL-DNA-F 1 1

1 SGSLsum-DNA-S-UL-DNA-F 1 1

1 SGSLsum-cDNA-S-UL-DNA-F 1 1

1 SS-DNA-S-UL-DNA-F 1 1

1 SS-cDNA-S-UL-DNA-F 1 1

1 SWL-DNA-F-UL-DNA-F 1 1

1 SWL-cDNA-F-UL-DNA-F 1 1

1 ArL-DNA-F-UL-cDNA-F 1 1

1 ArL-cDNA-F-UL-cDNA-F 1 1

1 LA-DNA-S-UL-cDNA-F 1 1

1 LA-cDNA-S-UL-cDNA-F 1 1

1 LL-DNA-F-UL-cDNA-F 1 1

1 LL-cDNA-F-UL-cDNA-F 1 1

1 ML-DNA-S-UL-cDNA-F 1 1

1 ML-cDNA-S-UL-cDNA-F 1 1

1 MR-DNA-F-UL-cDNA-F 1 1

1 MR-cDNA-F-UL-cDNA-F 1 1

1 NGSL-DNA-S-UL-cDNA-F 1 1

1 NGSLfall-DNA-S-UL-cDNA-F 1 1

1 NGSLspr-DNA-S-UL-cDNA-F 1 1

1 NGSLsum-DNA-S-UL-cDNA-F 1 1

1 PO-DNA-S-UL-cDNA-F 1 1

1 PO-cDNA-S-UL-cDNA-F 1 1

1 RL-DNA-F-UL-cDNA-F 1 1

1 SGSL-DNA-S-UL-cDNA-F 1 1

1 SGSL-cDNA-S-UL-cDNA-F 1 1

1 SGSLfall-DNA-S-UL-cDNA-F 1 1

1 SGSLfall-cDNA-S-UL-cDNA-F 1 1

1 SGSLspr-DNA-S-UL-cDNA-F 1 1

1 SGSLspr-cDNA-S-UL-cDNA-F 1 1

1 SGSLsum-DNA-S-UL-cDNA-F 1 1

1 SGSLsum-cDNA-S-UL-cDNA-F 1 1

1 SS-DNA-S-UL-cDNA-F 1 1

1 SS-cDNA-S-UL-cDNA-F 1 1

1 SWL-DNA-F-UL-cDNA-F 1 1

1 SWL-cDNA-F-UL-cDNA-F 1 1

1 UL-DNA-F-UL-cDNA-F 1 1


Output File Names: /Volumes/TOSHIBA EXT/Sequences/final.bacteria.an.thetayc.0.03.ave.tre.parsimony /Volumes/TOSHIBA EXT/Sequences/final.bacteria.an.thetayc.0.03.ave.tre.psummary"

As you can see… I have not values that differ from 1… My .design file looks lik:

jvert.01 NGSL-DNA-S
jvert.02 SGSL-DNA-S
jvert.03 LL-DNA-F
jvert.04 ArL-DNA-F
jvert.05 SS-DNA-S
jvert.06 MR-DNA-F
jvert.07 ML-DNA-S
jvert.08 LA-DNA-S
jvert.09 SWL-DNA-F
jvert.10 RL-DNA-F
jvert.11 UL-DNA-F
jvert.12 PO-DNA-S
jvert.13 NGSLspr-DNA-S
jvert.14 NGSLsum-DNA-S
jvert.15 NGSLfall-DNA-S
jvert.16 SGSLspr-DNA-S
jvert.17 SGSLsum-DNA-S
jvert.18 SGSLfall-DNA-S
jvert.19 SGSL-cDNA-S
jvert.20 LL-cDNA-F
jvert.21 ArL-cDNA-F
jvert.22 SS-cDNA-S
jvert.23 UL-cDNA-F
jvert.24 SWL-cDNA-F
jvert.25 LA-cDNA-S
jvert.26 ML-cDNA-S
jvert.27 MR-cDNA-F
jvert.28 PO-cDNA-S
jvert.29 SGSLspr-cDNA-S
jvert.30 SGSLsum-cDNA-S
jvert.31 SGSLfall-cDNA-S

Is there something I need to change? I know they are different because the .tre file makes a CLEAR tree.

Looking forward to your response!

2

The problem is you have no replication in your design file - every group is only represented by one sample. For any type of statistical analysis to work, you have to have some level of replication.