P A U P *
Version 4.0a126 for Macintosh (X86)
Thursday, February 21, 2013 12:05:43 PM Central Standard Time
Running on IA-32 architecture (64-bit word length)
SSE vectorization enabled
Multithreading enabled for likelihood using Pthreads
Compiled using Intel compiler (icc) 11.1.0 (build 20091012)
-----------------------------NOTICE----------------------------This is an alpha-test version prepared for the exclusive
use of course and workshop participants, as well as other
authorized testers. It will expire on 1 Aug 2013.
Please report bugs to david.swofford@duke.edu
---------------------------------------------------------------Processing of file "Seb Modified 21 Feb.nex" begins...
Data matrix has 27 taxa, 53 characters
Valid character-state symbols: 01234
Missing data identified by '?'
Gaps identified by '-'
Outgroup status changed:
3 taxa transferred to outgroup
Total number of taxa now in outgroup = 3
Number of ingroup taxa = 24
Heuristic search settings:
Optimality criterion = parsimony
Character-status summary:
Of 53 total characters:
All characters are of type 'unord'
All characters have equal weight
All characters are parsimony-informative
Gaps are treated as "missing"
Multistate taxa interpreted as uncertainty
Starting tree(s) obtained via stepwise addition
Addition sequence: simple (reference taxon = Antarctican taxon)
Number of trees held at each step = 1
Branch-swapping algorithm: tree-bisection-reconnection (TBR) with reconnection limit = 8
Steepest descent option not in effect
Initial 'Maxtrees' setting = 100
Branches collapsed (creating polytomies) if maximum branch length is zero
'MulTrees' option in effect
No topological constraints in effect
Trees are unrooted
Heuristic search completed
Total number of rearrangements tried = 48442
Score of best tree(s) found = 146
Number of trees retained = 2
Time used = 0.01 sec (CPU time = 0.01 sec)
Character types changed:
Of 53 total characters:
1 character is of type 'ord' (Wagner)
52 characters are of type 'unord'
*** Skipping "MESQUITECHARMODELS" block
*** Skipping "MESQUITE" block
Processing of input file "Seb Modified 21 Feb.nex" completed.
paup> HSearch;
Heuristic search settings:
Optimality criterion = parsimony
Character-status summary:
Of 53 total characters:
1 character is of type 'ord' (Wagner)
52 characters are of type 'unord'
All characters have equal weight
All characters are parsimony-informative
Gaps are treated as "missing"
Multistate taxa interpreted as uncertainty
Starting tree(s) obtained via stepwise addition
Addition sequence: simple (reference taxon = Antarctican taxon)
Number of trees held at each step = 1
Branch-swapping algorithm: tree-bisection-reconnection (TBR) with reconnection limit = 8
Steepest descent option not in effect
Initial 'Maxtrees' setting = 100
Branches collapsed (creating polytomies) if maximum branch length is zero
'MulTrees' option in effect
No topological constraints in effect
Trees are unrooted
Heuristic search completed
Total number of rearrangements tried = 48442
Score of best tree(s) found = 146
Number of trees retained = 2
Time used = 0.01 sec (CPU time = 0.00 sec)
paup> DescribeTrees all;
Tree description:
Unrooted tree(s) rooted using outgroup method
Optimality criterion = parsimony
Character-status summary:
Of 53 total characters:
1 character is of type 'ord' (Wagner)
52 characters are of type 'unord'
All characters have equal weight
All characters are parsimony-informative
Gaps are treated as "missing"
Multistate taxa interpreted as uncertainty
Character-state optimization: Accelerated transformation (ACCTRAN)
Tree number 1 (rooted using user-specified outgroup)
Tree length = 146
Consistency index (CI) = 0.3973
Homoplasy index (HI) = 0.6027
Retention index (RI) = 0.6966
Rescaled consistency index (RC) = 0.2767
/----------------------------------------------------------------------------------------------|
/-------+-------------------------------------------------------------------------------------31-------32
/-----------------------|
/-------------------------------------------------------------30
/---------------|
|
\------29
/-------|
|
\------28-------\------33
/------------------------------------------------------------------------------|
|
/-------\------34
/-------------------------------------------------------------35-------|
|
/-------------------------------|
|
/-----------------------------41
/-----------------------\------36
|
\------40
/-------|
|
|
/------37-------|
|
\------39
/-------\------42
\------38-------|
/-------|
/---------------------------------------------43-------\------44
/----------------------------------------------\------45
/---------------------------------------|
|
/-------\-----46
/----------------------52-------\------51
/-------|
/--------------47-------\------50
/---------------\------49
/-------\------48--------
Lydekkerina
Rhineceps
Uranocentrodon
Benthosuchus
Thoosuchus
Angusaurus
Trematosaurus
Wetlugasaurus
Vladlenosaurus
Odenwaldia
Parotosuchus
Calmasuchus acri
Cyclotosaurus
Tatrasuchus
Mastodonsaurus
Eryosuchus
Watsonisuchus
Edingerella
Xenotosuchus
Cherninia
Antarctican taxon
Paracyclotosaurus
St.pronus
St.birdi
Procycloto
Eocyclotosaurus
Quasicyclotosaurus
Tree number 2 (rooted using user-specified outgroup)
Tree length = 146
Consistency index (CI) = 0.3973
Homoplasy index (HI) = 0.6027
Retention index (RI) = 0.6966
Rescaled consistency index (RC) = 0.2767
/----------------------------------------------------------------------------------------------|
/-------+-------------------------------------------------------------------------------------31-------32
/-----------------------|
/-------------------------------------------------------------30
/---------------|
|
\------29
/-------|
|
\------28-------\------33
/------------------------------------------------------------------------------|
|
/-------\------34
/-------------------------------------------------------------35-------|
|
/---------------------------------------\------36
/---------------------41
/-------------------------------|
|
\------40
/-----------------------|
|
\------39
/---------------\------42
\------38
/-------|
\------37-------|
/-------|
/---------------------------------------------43-------\------44
/----------------------------------------------\------45
/---------------------------------------|
|
/-------\-----46
/----------------------52-------\------51
/-------|
/--------------47-------\------50
/---------------\------49
/-------\------48--------
Input data matrix:
11111111112222222222333333333344444444445555
Taxon
12345678901234567890123456789012345678901234567890123
------------------------------------------------------------------------Antarctican taxon
0?0??012?0111201110?10?011011110??1111?????????110?11
Angusaurus
11100111110100111011111110001000100110101111100000010
Benthosuchus
11001011010101110011010010001100110111100011000000010
Cherninia
010110020011120100000000111011111111111??????00101?10
Cyclotosaurus
010200020011110012001010111111111111111110???10101000
St.pronus
0101000200111201100000011111111111?1111100?1011001011
Eocyclotosaurus
11021012010112111001111011111110111111???????10001012
Mastodonsaurus
01010012011101011101100011111111111111111111000110010
Paracyclotosaurus
0101100200111201010?100?111111111111111100?1011111?11
Parotosuchus
01001002001112010100000011101111111111110011000000110
Tatrasuchus
0101?002001111000200000011101111111111111111010001100
Thoosuchus
11000111110100110011011110000000100110101111100000010
Trematosaurus
111001111101001110?11111???01001100?10101111100000010
St.birdi
01010002001112011000000111111111111111110011011001111
Rhineceps
00000000000001000000000000000000000001000000000000000
Quasicyclotosaurus 01021012010102101001001011?11110??0111???????10001012
Xenotosuchus
01011002001111011000000011101111?11111110011011100010
Procycloto
1102100200111201100?0???1??111?1111111???????01?01?11
2
Calmasuchus acri
0101000?0011?1?1?10100001?1011111????1110011000000101
Watsonisuchus
01001002001112010010000011101110111111110011011000010
Vladlenosaurus
1100100200011001001001001?10111???????11?11?000000010
Lydekkerina
01100001000101000000000010000100100010100011000000000
Odenwaldia
110010020??1110?0??1????????1???111?11???????00????10
Eryosuchus
01011002001111011100000011101111111111111011000110100
1
Wetlugasaurus
01001002000111010010010011101101011111111011000000010
1
Edingerella
01001002001111100000000010101010010?1101001?011000000
1
1
Uranocentrodon
0000000000000000000000000000010?000001000000000000000
paup> CStatus;
Lydekkerina
Rhineceps
Uranocentrodon
Benthosuchus
Thoosuchus
Angusaurus
Trematosaurus
Wetlugasaurus
Vladlenosaurus
Odenwaldia
Parotosuchus
Calmasuchus acri
Tatrasuchus
Eryosuchus
Cyclotosaurus
Mastodonsaurus
Watsonisuchus
Edingerella
Xenotosuchus
Cherninia
Antarctican taxon
Paracyclotosaurus
St.pronus
St.birdi
Procycloto
Eocyclotosaurus
Quasicyclotosaurus
Character-status summary:
Current optimality criterion = parsimony
No characters are excluded
Of 53 total characters:
1 character is of type 'ord' (Wagner)
52 characters are of type 'unord'
All characters have equal weight
All characters are parsimony-informative
paup> Log start;
Logging output to file "~/Documents/Manuscripts/ANT Manuscripts/Antarctosuchus MS/Fortuny
cladistics/Seb Modified
21 Feb.log".