Computational protocol: A set of highly informative rat simple sequence length polymorphism (SSLP) markers and genetically defined rat strains

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Protocol publication

[…] A phylogenetic tree of rat strains was obtained through maximum parsimony analysis implemented in PAUP 4.0b10 []. First, the allele size of the 357 SSLP markers was transformed to discrete characters in such a way that any size allele differed by one step. A heuristic search method was used in PAUP to search for optimal trees because the genotype data set for the 122 rat strains was too large for single-step computer analysis. Unordered characters were defined such that any state was capable of transforming directly to any other state with equal cost (Fitch parsimony). Two basic strategies are combined in the heuristic search strategy: a stepwise addition to obtain an initial tree, and branch swapping for rearrangement to find shorter trees. Under the analysis, 100 random addition-sequence replications were done, followed by a tree bisection-reconnection (TBR) branch swapping algorithm with the COLAPSE option on to collapse any zero-length branches and with the STEEPEST DESCENT option off. Tree stability was estimated by bootstrap analysis of 100 replicates, sampling characters with equal probability. TreeView [] was used to display the radial tree. […]

Pipeline specifications

Software tools PAUP*, PHYLIP, TreeViewX
Application Phylogenetics
Organisms Rattus norvegicus, Homo sapiens