PAUPPhylogenetic Analysis Using Parsimony
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The ML analysis was performed by a heuristic search with TBR branch swapping and 100 random additions of taxa, performed in PAUP 4.
Maximum Parsimony (MP) and Maximum Likelihood (ML) analysis were performed with PAUP 4.
A dendrogram was constructed using the neighbor-joining, maximum parsimony and maximum likelihood methods with PAUP software v4.
08 (Maddison & Maddison 2005) and analysed the matrix under the criterion of Maximum Parsimony using PAUP 4.
Pairwise sequence divergences were calculated in PAUP version 4.
A phylogenetic tree was estimated using the neighbor-joining (NJ) method in PAUP version 4.
Results of a PAUP * search using the ML criterion, with a necessarily reduced set of taxa, were consistent with those from the more extensive GARLI analysis (Fig.
6 (Posada & Crandall 1998) was run using the likelihood scores generated by PAUP under the "longfmt=yes" option of the Lscores command to determine the preferred maximum likelihood model.
AFLPs from 40 individuals were coded as presence-absence data and analyzed in PAUP.
The MP phylogenetic tree was generated by heuristic search routines with 1,000 random-addition sequences and TBR branch swapping using the software PAUP * 4.