Paup
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PAUP* 4.0
General description
PAUP* version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees. The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees. In addition, the PAUP manual has proven to be an essential guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field. With the inclusion of maximum likelihood and distance methods in PAUP* 4.0, the new version represents a great improvement over its predecessors. In addition, the speed of the branch-and-bound algorithm has been enhanced and a number of new features have been added, from agreement subtrees to tests for combinability of data and permutation tests for nonrandomness of data structure.
Application homepage
Proper citation
Swofford, D.L. (1998). PAUP: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0d64 ed, Sinauer Associates, Inc. Publishers, Sunderland, MA.
Input file formats
#NEXUS
[This file contains a simulated DNA data set followed by a PAUP
block with instructions to conduct a likelihood analysis. The following
numbered list corresponds with the numbered lines in the PAUP block.
(1) Construct a Neighbor Joining tree.
(2) Compute the likelihood of the NJ tree assuming the HKY85 model of sequence
evolution (Hasegawa, M., Kishino, H., and Yano, T., 19852) with gamma
distributed rates (Yang, 1994), where the transition/transversion rate ratio
and the shape parameter of the gamma distribution are estimated from the data
and empirical base frequencies are used.
(3) Change the optimality criterion to maximum likelihood.
(4) Set the parameter values to those that were estimated on the neighbor joining
tree.
(5) Conduct a heuristic search with five random addition sequences and TBR branch
swapping.
]
Begin taxa;
Dimensions ntax=8;
taxlabels
A
B
C
D
E
F
G
H
;
end;
Begin characters;
Dimensions nchar=200;
Format datatype=dna interleave;
Matrix
A CGAATATAACGGAGCCAGTACTCAGACGCACTGCCAACCCAGCGAAGCCCGATACGCCGT
B CGAATATAACGAAGCCAGTATTCAGACGCACTGCTAACCCAGCGGAGCCCGGTACGCCGT
C CGAATATAACAAAGCCAGTACTCGGACGCACTACCAACCCAGCGGAGCCCGATACGCCAT
D CGAATACAACAAAGCCAGTATTCAGACGCACTGCCAACCCAACAGAGACCGGCGTGCTAT
E CGAATACAACAAAGCCAGTATTCAGACGCACTGCCAACCCAGCAGAGACCCCCACGCTAT
F CGAATACAACAAAGCCAGTATTCAGACGCACTGCCAACCCAGCAGAGACCCACACGCTAT
G CGAATACAACAAAGCCAATATTCAGACGGACTGCCAACCCAGCAGAGACCGACACGTCAT
H CGAATACAACAAAGCCAATATTCAGACGGACTGCCAACCCGGCAGAGACCGACGCGTCAT
A CGCATGAACGCTCTCCGCATGCAAAGTCCAACAAGTCAAACGGGATTCGGATCGTGCACG
B TGCGTGGACGTTCCTCGCTCACAAGGTCGAGCAGTTCAAACGAGGATTGGAGCGTACAAC
C AAGATGCACATTTTCCGTAGATAAAACCGAAACATTCAAGCGAATGCTACACCTAACGGC
D AAAATGTATAACTTCCGTGCACAAAACCAAAAAACCCAAGCGGACAATAAGATACGCGGC
E AACACACACGACGCCCGTAAACAAAACTAAAAAAGCCGACCAGGCGTACGAGGACAGAAT
F AAGATACATGATACCCGGGCACAAAACCAGAAAAGCCGACCGAATGTGTAAGCGCCAAGT
G AAAACACATTAATGCCGTACACAGGACCAAAACATTCAAAAGGAACGGTAGCTATAACAA
H AAAATACATGATTCCCGTACACAAAATCACAAAATCCAAACGAAGGAGTTAATACGGAAC
A AATGGTGATTGCGAACTCAAGTCAAGCACAACTCTGAGCATTCCTGAAACTACTGGAGAC
B AATGCCCAACATCACTTCCACTAAAACCCCGCTCTGCACCGCACGACAGAACGACACTGA
C GGGGTTAGTCGAAAGACTATCCAGAACGGAATTACCTGGATCGCTAGGACAAAACAGAGG
D GAATGATACCTAAGAACCGCGCGGACTAATAAGACACGCTCTGATGCAGGCCTGCCGAAA
E ACACTATGCGTCATGAAAGTCTGCTCCGACAGGATTTGTCTTACGCGTTCTCACCTATAG
F GAAGACTGCGCCACCGACATCTGATGCACCACTGTCTGTACAGCGCCAGCGGAATACGGC
G AGCCATCGCCTAAGTAAAGCCCAGCACAGTATGTGCCGTCCTTCTCATATAACTCTCACG
H AGGCAGCACTTGGGCCTGGCTTAGAATGTCGCGCACAACAATACCAATGAACATCGACCC
A CATTTGAAGACGATCAAAAT
B CACGGCCAACAACGTAAAGC
C ACTAGGATCTCTAGTATTAG
D ATGCAAGCCAAAAGTGTGAT
E GATAGAATTGAGAATAACTC
F CGCGCAGCAAATGCCCGATC
G AACATCTCAGACTCGACAGA
H AAGCAACTCCCCACAGAAAC
;
End;
BEGIN PAUP;
[1] NJ;
[2] LSCORE 1/ BASEFREQ=empirical TRATIO=estimate RATES=gamma SHAPE=estimate;
[3] SET CRITERION=like;
[4] LSET BASEFREQ=empirical TRATIO=previous RATES=gamma SHAPE=previous;
[5] HSEARCH ADDSEQ=random NREPS=5 SWAP=TBR;
END;
Speeding up PAUP*
Accelerating maximum-likelihood searches using PAUP*: A description of how to minimize runtime and optimize ML analysis in PAUP*
Documentation
Manual: http://paup.csit.fsu.edu/downl.html#Anchor-58521
Quick Start: http://paup.csit.fsu.edu/Quick_start_v1.pdf
Q&A: An interactive website where questions and answers can be posted by participates. This is probably the fastest way to find or get an answer to your question: http://pauptech.csit.fsu.edu/%7epaupforum
Information list Paupinfo: http://lists.csit.fsu.edu/mailman/listinfo/paupinfo
Known problems�: http://paup.csit.fsu.edu/problems.html
FAQ: http://paup.csit.fsu.edu/paupfaq/faq.html
Useful hints
PAUP* 4.0 and the MacClade 4.0 (alignment- and tree editing program; for Mac only) use a common data file format (NEXUS), allowing easy interchange of data between the two programs