Phylogenetic analysis parsimony methods

Swofford D. L. (2000). PAUP. Phylogenetic Analysis Using Parsimony ( and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts. 

The home page of WebPhylip consists of three windows. The left window is the command window for selecting and issuing the execution (Run) of the analysis/ operation. The analysis results appear in the upper window. The lower window is the query window with options, a query box for pasting the query sequences (in Phylip format), and Submit/Clear buttons. To perform phylogenetic analysis, select DNA/Protein for Phylogeny method in the left window to open the available analytical methods (parsimony, parsimony + branch bound, compatibility, maximum likelihood, and maximum likelihood with molecular clock for DNA whereas only parsimony for protein). Click Run (under the desired method) to open the query window with options. Select the appropriate Input type (either interleaved or sequential), paste the query sequences and click the Submit button. The analytical results are displayed in the upper window (Figure 13.4). 

Strimmer K, von Haeseler A (1997) Likelihood mapping a simple method to visualize phylogenetic content of a sequence alignment. ProcNatl Acad Sci USA 94 6815-6819 Swofford DL (1998) PAUP - phylogenetic analysis using parsimony ( and other methods), version 4.0. Sinauer, Sunderland... 

Stefels J (1997) The smell of the Sea. Production of dimethylsulphoniopropionate and its conversion into dimethylsulphide by the marine phytoplankton genus Phaeocystis. Dissertation, University of Groningen Swofford DL (2002) PAUP Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta, Florida State University, CD-ROM... 

Bootstrapping is a resampling tree evaluation method that works with distance, parsimony, likelihood, and just about any other tree derivation method. It was invented in 1979 (Efron, 1979) and introduced as a tree evaluation method in phylogenetic analysis by Felsenstein (1985). The result of bootstrap analysis is typically a number associated with a particular branch in the phylogenetic tree that gives the proportion of bootstrap replicates that supports the monophyly of the clade. 

The third (default) method uses a table of empirically observed transitions between amino acids (the Dayhoff PAM 001 matrix). The character-based analysis of sequence data can be initiated via the appropriate executable file (e.g. DnaPars, DnaML or ProtPars). PHYLIP comprises DnaPars and DnaML to estimate phylogenetic relationships by the parsimony method and the maximum likelihood methods from nucleotide sequences respectively. ProtPars is the parsimony program for protein sequences. 

Several phylogenetic analysis programs use a generalized parsimony method in which the user (Swofford 1990, Maddison and Maddison 1990) or the program (Williams and Fitch 1989) defines a matrix which describes the cost associated with a transition from state i to state j.. Modification of the cost matrix allows experimentation with different kinds of weighting. 

Souza-Chies, T. T., Bittar, G., Nadot, S., Carter, L., Besin, E. and Lejeune, B. (1997) Phylogenetic analysis of Iridaceae with parsimony and distance methods using the plastid gene rps4. Plant Systematics and Evolution, 204 109-123. 

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