Evolutionary Tree: Difference between revisions
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'''BACKGROUND''' | |||
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Cladogram_view.JPG Cladogram view] | [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Cladogram_view.JPG Cladogram view] | ||
In detecting evolunationary tree, BLAST was used to searching homologous sequence. In addition, Clustal X was used to align the sequence specifically by using multiple alignment method. Phylogenetic analysis was conducted using treeview program follows with editing the tree to adding the boostrap value. | In detecting evolunationary tree, BLAST was used to searching homologous sequence. In addition, Clustal X was used to align the sequence specifically by using multiple alignment method. Phylogenetic analysis was conducted using treeview program follows with editing the tree to adding the boostrap value. | ||
'''FINAL TREE ANALYSIS''' | |||
[http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Radial.JPG Evolutionary analysis of the tree with radial view] | [http://compbio.chemistry.uq.edu.au/mediawiki/index.php/Image:Radial.JPG Evolutionary analysis of the tree with radial view (professional viewer) ] | ||
Legends: | Legends: | ||
* red dot signs near the branch means boostrap value more than 75% | * red dot signs near the branch means boostrap value more than 75% | ||
* different color in branching tree represent | * different color in branching tree represent how two or more species is closely related | ||
* any number located near boostrap value means the confidence | * any number located near branching tree means boostrap value of the branching tree | ||
'''IN DEPTH UNDERSTANDING''' | |||
SNAP-gamma protein evolutionary tree mostly contains more than 75% boostrapvalue. Thus, red dot signs was assign to represent more than 75% boostrap value. The value was indicated the degree confidence of the branching tree. As an example: 80.0 boostrap value means we are 80% confidence about the splitting tree path into specific species. On the other hand, low boostrap value represent low confidence of the path of branching tree. | |||
Two or more species which is closely related was assign with same color of the branch tree. | |||
Revision as of 01:55, 2 June 2007
BACKGROUND
In detecting evolunationary tree, BLAST was used to searching homologous sequence. In addition, Clustal X was used to align the sequence specifically by using multiple alignment method. Phylogenetic analysis was conducted using treeview program follows with editing the tree to adding the boostrap value.
FINAL TREE ANALYSIS
Evolutionary analysis of the tree with radial view (professional viewer)
Legends:
- red dot signs near the branch means boostrap value more than 75%
- different color in branching tree represent how two or more species is closely related
- any number located near branching tree means boostrap value of the branching tree
IN DEPTH UNDERSTANDING SNAP-gamma protein evolutionary tree mostly contains more than 75% boostrapvalue. Thus, red dot signs was assign to represent more than 75% boostrap value. The value was indicated the degree confidence of the branching tree. As an example: 80.0 boostrap value means we are 80% confidence about the splitting tree path into specific species. On the other hand, low boostrap value represent low confidence of the path of branching tree.
Two or more species which is closely related was assign with same color of the branch tree.
