P A U P *

Version 4.0a152 for 32-bit Microsoft Windows (built on Jan 26 2017 at 21:47:42)
Thu Jun 15 06:03:30 2017

Running on IA-32 architecture (64-bit word length)

SSE vectorization enabled
Multithreading enabled for likelihood using Pthreads

-----------------------------NOTICE-----------------------------
This is an alpha-test version that is still changing rapidly.
It will expire on 1 Jul 2017.

Please report bugs to david.swofford@duke.edu

----------------------------------------------------------------

Processing of file "C:\Users\Ijat\Desktop\Master Atul\Morphology PAUP.nex.txt"

begins...

Data matrix has 17 taxa, 50 characters

Valid character-state symbols: 012345678
Missing data identified by '?'

Processing of input file "Morphology PAUP.nex.txt" completed.

paup> Set criterion=distance;

Optimality criterion set to distance.

Pairwise distances between taxa

Below diagonal: Total character differences

Above diagonal: Mean character differences

1 2 3 4 5 6 7 8
9 10
1 Tectona grandis - 0.46000 0.48000 0.56000 0.46000 0.58000 0.44000 0.48000
0.44000 0.46000
2 C breviflorum 23 - 0.20000 0.30000 0.28000 0.42000 0.24000 0.28000
0.24000 0.26000
3 C laevifolium 24 10 - 0.18000 0.18000 0.42000 0.20000 0.24000
0.20000 0.14000
4 C deflexum 28 15 9 - 0.28000 0.44000 0.22000 0.20000
0.24000 0.26000
5 C hendersonii 23 14 9 14 - 0.40000 0.18000 0.32000
0.22000 0.20000
6 C paniculatum 29 21 21 22 20 - 0.44000 0.34000
0.42000 0.34000
7 C indicum 22 12 10 11 9 22 - 0.24000
0.14000 0.18000
8 C nutan 24 14 12 10 16 17 12 -
0.20000 0.16000
9 C phyllomega 22 12 10 12 11 21 7 10
- 0.22000
10 C umbellatum 23 13 7 13 10 17 9 8
11 -
11 C villosum 27 21 22 24 21 18 22 19
24 18
12 C chinense 33 31 29 28 29 24 30 28
31 29
13 C disparifolium 21 12 10 13 13 23 9 11
10 8
14 C johorense 23 15 14 12 16 23 14 10
11 13
15 C myhensis 22 14 12 12 15 24 13 11
10 14
16 C speciesone 24 14 12 13 14 16 10 9
13 6
17 C speciestwo 25 13 8 10 12 16 10 9
10 5

Pairwise distances between taxa (continued)

Below diagonal: Total character differences

Above diagonal: Mean character differences

11 12 13 14 15 16 17
1 Tectona grandis 0.54000 0.66000 0.42000 0.46000 0.44000 0.48000 0.50000
2 C breviflorum 0.42000 0.62000 0.24000 0.30000 0.28000 0.28000 0.26000
3 C laevifolium 0.44000 0.58000 0.20000 0.28000 0.24000 0.24000 0.16000
4 C deflexum 0.48000 0.56000 0.26000 0.24000 0.24000 0.26000 0.20000
5 C hendersonii 0.42000 0.58000 0.26000 0.32000 0.30000 0.28000 0.24000
6 C paniculatum 0.36000 0.48000 0.46000 0.46000 0.48000 0.32000 0.32000
7 C indicum 0.44000 0.60000 0.18000 0.28000 0.26000 0.20000 0.20000
8 C nutan 0.38000 0.56000 0.22000 0.20000 0.22000 0.18000 0.18000
9 C phyllomega 0.48000 0.62000 0.20000 0.22000 0.20000 0.26000 0.20000
10 C umbellatum 0.36000 0.58000 0.16000 0.26000 0.28000 0.12000 0.10000
11 C villosum - 0.46000 0.40000 0.46000 0.52000 0.42000 0.38000
12 C chinense 23 - 0.62000 0.68000 0.62000 0.58000 0.56000
13 C disparifolium 20 31 - 0.22000 0.24000 0.22000 0.20000
14 C johorense 23 34 11 - 0.14000 0.28000 0.24000
15 C myhensis 26 31 12 7 - 0.30000 0.30000
16 C speciesone 21 29 11 14 15 - 0.14000
17 C speciestwo 19 28 10 12 15 7 -

paup> NJ;

Neighbor-joining search settings:

Ties (if encountered) will be broken systematically
Distance measure = mean character difference
50 characters are included
(Tree is unrooted)

Neighbor-joining tree:

/------------------------------------------ Tectona grandis

|
| /----------------------- C breviflorum
| |
| | /------------- C laevifolium
| | /--+
| | | \------------------- C deflexum
| | |
| | /+ /------- C umbellatum
| | || /+
| | || |\------------- C speciesone
| /------+ |\-----+
| | | /+ \--------- C speciestwo
| | | ||
| | | || /---------------- C nutan
| | | || |
| | | |\--+ /------------ C johorense
| | | | \--------+
| | | | \------------ C myhensis
| | | |
\---------+ \--+----------------- C disparifolium
| |
| | /-------------------- C hendersonii
| | /-+
| | | \------------ C indicum
| \--+
| \------------- C phyllomega
|
| /--------------------------- C paniculatum
| |
\-------------+ /-------------------------- C villosum
\----+
\-----------------------------------------------------
- C chinense

Tree found by neighbor-joining method stored in tree buffer

Note: Ties were encountered; neighbor-joining tree may not be unique
Time used for tree calculation = 0.00 sec (CPU time = 0.00 sec)

paup> Bootstrap nreps=500;

Bootstrap method with heuristic search:

Number of bootstrap replicates = 500
Starting seed = generated automatically
Number of characters resampled in each replicate = 50
Optimality criterion = distance (unweighted least squares (power=0))
Negative branch lengths allowed, but set to zero for tree-score calculation
Distance measure = mean character difference
50 characters are included
Starting tree(s) obtained via neighbor-joining
Branch-swapping algorithm: tree-bisection-reconnection (TBR) with reconnection
limit = 8
Steepest descent option not in effect
Initial 'Maxtrees' setting = 100
Zero-length branches not collapsed
'MulTrees' option in effect
No topological constraints in effect
Trees are unrooted

500 bootstrap replicates completed

Time used = 4.61 sec (CPU time = 4.56 sec)

Bootstrap 50% majority-rule consensus tree

/-------------------------------------------------------------------------------
Tectona grandis(1)
|
| /--------------------------------------- C
breviflorum(2)
| |
| +--------------------------------------- C
laevifolium(3)
| |
| +--------------------------------------- C
deflexum(4)
| |
| +--------------------------------------- C
hendersonii(5)
| |
| +--------------------------------------- C
indicum(7)
| |
| +--------------------------------------- C
nutan(8)
| |
| /--------59---------+--------------------------------------- C
phyllomega(9)
| | |
| | +--------------------------------------- C
umbellatum(10)
| | |
| | +--------------------------------------- C
disparifolium(13)
| | |
| | | /-------------------- C
johorense(14)
| | +--------84--------+
\-------------------+ | \-------------------- C
myhensis(15)
| |
| +--------------------------------------- C
speciesone(16)
| |
| \--------------------------------------- C
speciestwo(17)
|
| /--------------------------------------- C
paniculatum(6)
| |
\--------87---------+ /-------------------- C
villosum(11)
\--------60--------+
\-------------------- C
chinense(12)

Bipartitions found in one or more trees and frequency of occurrence (bootstrap

support values):

1 1
12345678901234567 Freq %
----------------------------------------
.....*....**..... 433.00 86.60%
.............**.. 421.17 84.23%
..........**..... 299.50 59.90%
.****.****..***** 292.50 58.50%
.........*.....** 192.50 38.50%
.........*.....*. 149.00 29.80%
......*.*........ 145.50 29.10%
.........*......* 141.50 28.30%
.....*.....*..... 140.00 28.00%
..**............. 121.00 24.20%
...*.........**.. 119.00 23.80%
........*....**.. 109.67 21.93%
.***..****..***** 105.00 21.00%
....*.*.......... 103.00 20.60%
...............** 101.00 20.20%
...*...*.....**.. 81.50 16.30%
....*.*.*........ 74.00 14.80%
.**.............. 73.50 14.70%
...*...*......... 72.00 14.40%
......*.....*.... 64.50 12.90%
.......*.*.....** 64.50 12.90%
.****.*.*........ 61.00 12.20%
..*.*............ 61.00 12.20%
..***.****..***** 57.00 11.40%
..******.***...** 57.00 11.40%
.......*.....**.. 53.33 10.67%
..*......*....... 51.00 10.20%
.....*....*...... 49.50 9.90%
..*......*.....** 49.00 9.80%
.......**....**.. 48.00 9.60%
...*..***...***.. 48.00 9.60%
..**..****..***** 47.00 9.40%
............***.. 44.00 8.80%
.****.*.*...***.. 43.00 8.60%
..*......*......* 42.00 8.40%
.*********..***** 40.00 8.00%
...*...**....**.. 40.00 8.00%
.....*.*.***...** 39.00 7.80%
.....*.*..**..... 36.00 7.20%
.*..........*.... 36.00 7.20%
....**....**..... 36.00 7.20%
..**.........**.. 35.50 7.10%
.......*.*.....*. 32.50 6.50%
.***********.**** 30.50 6.10%
...*.*.*..**..... 30.00 6.00%
.*******.***...** 29.50 5.90%
.**.*............ 29.00 5.80%
.........*..*..** 28.00 5.60%
....*.*.*....**.. 28.00 5.60%
.****.*.*....**.. 27.00 5.40%
..**............* 27.00 5.40%
.*....*.....*.... 26.00 5.20%
...*.*.*.***...** 25.00 5.00%

542 groups at (relative) frequency less than 5% not shown

paup> DescribeTrees / brLens=yes;

Tree description:

Unrooted tree(s) rooted using outgroup method

Note: No outgroup has been defined; tree is (arbitrarily) rooted at first taxon.
Optimality criterion = distance (unweighted least squares (power=0))
Negative branch lengths allowed, but set to zero for tree-score calculation
Distance measure = mean character difference
50 characters are included

Tree 1 (rooted using default outgroup)

Branch lengths and linkages for tree #1 (unrooted)

Connected Branch
Node to node length
---------------------------------------------
Tectona grandis (1) 22 0.29179
19 22 0.06151
C breviflorum (2) 19 0.14337
C laevifolium (3) 19 0.09670
C deflexum (4) 19 0.13270
C hendersonii (5) 19 0.13270
C indicum (7) 19 0.10070
C nutan (8) 19 0.09803
C phyllomega (9) 19 0.10470
C umbellatum (10) 19 0.07670
C disparifolium (13) 19 0.10470
18 19 0.08235
C johorense (14) 18 0.06933
C myhensis (15) 18 0.07067
C speciesone (16) 19 0.10870
C speciestwo (17) 19 0.08337
21 22 0.07440
C paniculatum (6) 21 0.15857
20 21 0.03143
C villosum (11) 20 0.15000
C chinense (12) 20 0.31000
---------------------------------------------
Sum 2.48241

Sum-of-squares = 0.16281 (%SD=11.25641, g%SD=12.32764[k=21])

/----------------------------------------------------------------------------------
- Tectona grandis
|
| /----------------------------------------
- C breviflorum
| |
|
+----------------------------------------- C laevifolium
| |
|
+----------------------------------------- C deflexum
| |
|
+----------------------------------------- C hendersonii
| |
|
+----------------------------------------- C indicum
| |
|
+----------------------------------------- C nutan
| |
| /-------------------
19----------------------------------------- C phyllomega
| | |
| |
+----------------------------------------- C umbellatum
| | |
| |
+----------------------------------------- C disparifolium
| | |
| |
| /--------------------- C johorense
| | +------------------18
\-------------------22
| \--------------------- C myhensis
| |
|
+----------------------------------------- C speciesone
| |

| \----------------------------------------- C speciestwo
|

| /----------------------------------------- C paniculatum
| |
\-------------------
21 /--------------------- C villosum
\------------------20
\--------------------
- C chinense