TreeBASE Search-Analyses for study 10425

Delicious

Analyses for Study 10425

Citation title: "Phylogenetic studies in the Commelinaceae subfamily Commelinoideae inferred from Nuclear Ribosomal and Chloroplast DNA Sequences".

Study name: "Phylogenetic studies in the Commelinaceae subfamily Commelinoideae inferred from Nuclear Ribosomal and Chloroplast DNA Sequences".

This study is part of submission 10415 (Status: Published).

Analyses

Analysis 1

Analysis details

Name

Input data

1 Input object(s)

Analysis step

maximum likelihood Commelinaceae, trnL-trnF, Fig. 1 --

Output data

1 Output object(s)

Analysis 2

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Maximum Likelihood 5S NTS, Commelina 1, Fig. 2A --

Step details

Name

Software used

Name
Version
Algorithm
Commands
BEGIN PAUP; log file=log_Part_Comm1_5S_6_24_07.txt replace start; Execute Commelina1_5S_Fig2; exclude 82-121 204-353 390-411 439-444 490-509; set criterion=likelihood; Lset Base=(0.2108 0.2913 0.1951) Nst=6 Rmat=(1.0000 2.4630 1.0000 1.0000 1.5773) Rates=gamma Shape=1.8368 Pinvar=0; hsearch nreps=1 addseq=random swap=tbr start=stepwise; savetrees file=Part_Comm1_5S_6_24_07.tre brlens; log stop; END;

Output data

1 Output object(s)

Analysis 3

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Maximum Likelihood 5S NTS, Commelina 2, Fig. 2B --

Step details

Name

Software used

Name
Version
Algorithm
Commands
BEGIN PAUP; log file=log_Comm2_5S_ML.txt replace start; Execute Commelina2_5S_Fig3; delete Commelina_schliebenii; delete Commelina_coelestis; set criterion=likelihood; Lset Base=(0.1846 0.2867 0.2801) Nst=6 Rmat=(2.7983 6.0493 2.2343 1.4383 4.0522) Rates=gamma Shape=2.0204 Pinvar=0; hsearch nreps=1 addseq=random swap=tbr start=stepwise; savetrees file=Comm2_5S_ML.tre brlens; log stop; END;

Output data

1 Output object(s)

Analysis 4

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Maximum Likelihood 5S NTS, Callisia, Fig. 2C --

Step details

Name

Software used

Name
Version
Algorithm
Commands
BEGIN PAUP; log file=log_5S_Callisia_ML.txt replace start; Execute 5S_Callisia_ML.Paup; exclude 46-120; set criterion=likelihood; Lset Base=(0.1944 0.4005 0.1216) Nst=6 Rmat=(21.3752 96.6466 8.7655 28.4613 26.4276) Rates=gamma Shape=1.5545 Pinvar=0; hsearch nreps=1 addseq=random swap=tbr start=stepwise; savetrees file=5S_Callisia_ML.tre brlens; log stop; END;

Output data

1 Output object(s)

Analysis 5

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Maximum Likelihood 5S NTS, Murdannia, Fig. 2D --

Output data

1 Output object(s)

Analysis 6

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Maximum Likelihood 5S NTS, Tradescantia, Fig. 2F --

Output data

12 Output object(s)

Analysis 7

Analysis details

Name

Input data

1 Input object(s)

Analysis step

Maximum Likelihood, Combined trnL-trnF and 5S NTS, Commelinaceae --

Step details

Name
Notes

Software used

Name
Version
Algorithm
Commands
BEGIN PAUP; log file=log_Comm2_6_24_07.txt replace start; Execute Combined_Comm2_Partitions; exclude 1-985 986-1446 1447-3422; set criterion=likelihood; charpartition genes= LF:3423-4236, 5S:986-1446; Lset Base=(0.3228 0.1991 0.1240) Nst=6 Rmat=(1.3669 3.3089 0.0001 3.6357 8.3906) Rates=equal Pinvar=0; hsearch nreps=1 addseq=random swap=tbr start=stepwise; savetrees file=Part_Comm2_6_24_07.tre brlens; log stop; END;

Output data