ClustalX
ClustalX is the program that is used to align the different mitochondrial genome sequences. This program can make multiple alignments. The genome sequences were downloaded from the NCBI website (and from the made database) these were in FASTA format loaded into the program (Jeanmougina, Thompsona, Gouy, Higgins, & Gibson, 1998). ClustalX performs a global-multiple sequence alignment by the progressive method. The steps are:
1) Perform pair-wise alignment of all the sequences by dynamic programming
2) Use the alignment scores to produce a phylogenetic tree by neighbour-joining
3) Align the multiple sequences sequentially, guided by the phylogenetic tree (Tuimala, 2004)
There were two different alignments made. The first one contains the whole mitochondrial genome sequence from each species of the Ursidae. From each species the mitochondrial information of only one Animal is used for this alignment. The second alignment is based on the sequence of the cytochrome b part of the mitochondrial genome. For this alignment the cytochrome b sequence of multiple animals from each species (when it was available) was used.
TreeView
The alignment of the program ClustalX were loaded in the program TreeView. This is a program for displaying and printing phylogenies. TreeView can read the format that ClustalX made of the alignment and makes a phylogenic tree of this information (Page R. D., 1996). The phylogenetic trees are shown in an rectangular cladogram, because this is the mostly used cladogram in the literature its than easily to compare (Page R. D., 2002). There are two different phylogenetic trees made with TreeView, one of each alignment made in ClustalX.