Phylogenetic analysis using parsimony has made it the most widely used software package for the inference of evolutionary trees. To set up a paup spread sheet for rflp or rapd analyses. The trees were imported into paup 40b10 to construct the 50. Phylogeny programs continued university of washington. Henry paup historical records and family trees myheritage. This command loads the sequences from the nexus file into memory.
Some features in rainbow, including mrf and mincut supertree construction, are available even if paup is not installed. Maximum likelihood ml and maximum parsimony mp analyses were conducted using paup 4. The commonest am661 haplotype was present in 5 specimens from 4 geographical regions of thailand representing north, west, central and south thailand as well as 4 specimens from malaysia. In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of characterstate changes is to be preferred. Sitewise loglikelihoods of all hypotheses were first calculated with paup 4. The best model and parameter settings were chosen according to the akaike information criterion aic as suggested by modeltest v3. The simplot computer program 29 was used to analyze the alignment of the five. The asterisk in the name paup means and other methods. A unit in the division of the vice president for research.
The name paup means phyogenetic analysis using parsimony because parsimony was the only optimality criterion employed at the time. The molecular phylogenetic trees of the ssu rrna, lsu rrna, and cox2 genes and the threegenescombined tree were processed with paup4. If the nexus file had contained any commands, then these would also have been executed. With the inclusion of maximum likelihood and distance methods in paup 4. The program lies within education tools, more precisely science tools. When ready, it will be the primary site for the paup application. Branch lengths were estimated by constrained ml analysis using paup4. Sequence data from four intergenic spacer regions petapsbj, psbdtrnt. However, the neighborjoining nj analyses were done based on substitution model using paup4. The primary method used for singular value decomposition in paup is the dgesdd routine from the lapack library which is also used by r, matlab, and much other numerical software. Today were going to use paup to generate trees using distance methods. Paup is an application for phylogenetic analysis that uses parsimony.
Parsimony bootstrap analyses were performed using the full heuristic search option, random stepwise addition and replicates with maxtrees set at 5000 will not be increased. Evolution of the deepsea gulper eel mitochondrial genomes. Phylogenetic analysis using parsimony and other methods,version 4. Paup phylogenetic analysis using parsimony and other methods is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods swofford 2003. Madison, wi and phylogenetic analysis was performed with paup4. Aaron was born on june 15 1837, in york, pennsylvania, united states.
Molecular phylogeny of an unidentified haliphthoroslike. Originally, as the name implies, paup only implemented parsimony, but from version 4. Next in the output is paups summary of the winning sites test and the templeton test. Paup and produced by paup aircraft, introduced in 1982. The reliability of the obtained clades was tested by 500 bootstrap replications. Morphological and phylogenetic characterization of novel. The ml analyses with the nucleotide data set were conducted with paup4. The clades appear in resulted trees resembles the morphological similarities. The combined sequence alignments were obtained from mega7 version 7. Paup is licensed to individual users for the sole purpose of facilitating the scientific. Complete chloroplast genome of the genus cymbidium. The file is in the socalled nexus format that is widely used by phylogenyrelated software.
After paup starts, it will present you with an open dialog box. Education software downloads paup by david swofford and many more programs are available for instant and free download. Maximum parsimonybased phylogeny construction was performed using heuristic searches that consisted of tree bisection and reconnection tbr branch swapping in paup4. The paup phylogenetic analysis using parsimony software, created by. Under the maximumparsimony criterion, the optimal tree will minimize the amount of homoplasy i. Paup phylogenetic analysis using parsimony and other methods is a computational phylogenetics program for inferring evolutionary trees phylogenies, written by david l.
I have used various software programs for construction of the tree like paup, mesquite, biodiversitypro, etc. This tutorial was written primarily to help students in my laboratory to develop software that they can later modify for their own purposes, but i hope it is more. The goal of this lab exercise is to show you how to conduct maximum likelihood analyses in paup using several models, and to decide among competing models using likelihood ratio tests. Paup phylogenetic analysis using parsimony and other methods is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods. All gaps were treated as missing for ssu rrna, lsu rrna, and cox2 gene trees. Citeseerx scientific documents that cite the following paper. Addressing gene tree discordance and nonstationarity to resolve. Weve discussed distance methods in class, and you have learned that they are not the most theoretically justified of methods for inferring phylogenies, although clustering methods do have some uses in other areas of statistics. First, maximum parsimony analyses are performed for each data set and all most parsimonious trees are saved with their respective branch lengths. This file contains hepatitis c virus hcv sequences isolated from 4 different patients. Before doing any analyses, lets take a look at the data le paup just executed 1 open the algae.
Henry paup was born circa 1860, at birth place, pennsylvania, to aaron paup and sarah paup born witmer. Numerals indicate bayesian posterior probabilities shown as percentages. The asterisk in the name paup means and other methods, which were added later. We have discovered that the singular values returned by this function can be inaccurate for sparse flattening matrices containing many zero entries i. Phylogenetic analysis of turkey astroviruses reveals evidence of. Conventions filename or taxon name is a file or taxon that you must give. The scale indicates expected nucleotide substitutions per site. Molecular phylogeny of the subgenus ceratotropis genus vigna. Paup is used to infer mrp supertrees, and to calculate some tree distance measures. Paup is listed in the worlds largest and most authoritative dictionary database of abbreviations and acronyms the free dictionary. Neighborjoining analyses of aligned nucleotide sequences using paup4. Successfully load course software onto a mac in room 112 old hort. Once the system has moved you to a compute node, type the following commands to start the paup program. Looking for online definition of paup or what paup stands for.
Phylogenetic analysis using parsimony and other methods. Phylogenetic software development tutorial version 2 paul o. Most phylogenetic programs used for phylogenetic reconstruction operate. The paup pcraft is an american ultralight aircraft that was designed by d. The aircraft was supplied as a kit for amateur construction. Download limit exceeded you have exceeded your daily download allowance. Paup activity table of contents expected learning outcome getting started exercise 1. Jan 30, 2012 the name paup means phyogenetic analysis using parsimony because parsimony was the only optimality criterion employed at the time. Documentation faq frequently asked questions help and support news and updates community blog about contact. This will give you a prompt paup where you can write commands to the program. Lewis and being used in biol 848 with slight modifications by mark holder with pauls permission. Learn the differences between heuristic, branchandbound, and exhaustive search options.
Because of the 8way tie for the low ranks and the 2 way tie for the high ranks, we use the means. So the low ranked characters would have a rank of 4. Paup is a new release of the software package for inference of evolutionary trees, for use in macintosh, windows, unixvms, or dosbased. Today were going to use paup to generate trees using. Phylogenetic analysis using parsimony and other methods, version 4.
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