This figure presents result files from ClustalW.
#BIOEDIT MAKE A TREE PC#
It automatically downloads to your PC or laptop. This figure represents the result from clustalW, and you can save result to the computer by right clicking the file and selecting “save target as”. Upload the file(al.txt) from computer, and then click the run butoon to let the clustalw execute Scroll down the web page to the upload region Alignment & Phylogenetic tree construction Open website “.th” and type “clustalw” in the search box. These are whole FASTA formats from NCBI database including human, Neanderthal, chimpanzee, gorilla, orangutan, siamang, and bonobo.Īfter saving, the prepared file(al.txt) appears on the desktop. Type “mitochondrial D-loop hypervariable region I bonobo” in the search box. Type “mitochondrial D-loop hypervariable region I siamang” in the search box. Type “mitochondrial D-loop hypervariable region I orangutan” in the search box. Type “mitochondrial D-loop hypervariable region I gorilla” in the search box.Īfter searching completely, click the first sequence. Type “mitochondrial D-loop hypervariable region I chimpanzee” in the search box.Īfter searching completely, click the second sequence. Try to find more relevant sequence, I go to next page as shown in the figure, and choose sequence in the red oval mark. Type “mitochondrial D-loop hypervariable region I human” in the search box.Īfter searching completely, click the nucleotide panel.
![bioedit make a tree bioedit make a tree](https://people.bath.ac.uk/bsssjc/bioinf_pg.bho/bioinf2_pict/pdb_search_2016.jpg)
I prefer to use FASTA format and save to notepad program.
![bioedit make a tree bioedit make a tree](http://4.bp.blogspot.com/-L0YgKwDTqYU/Tz7h86YJmwI/AAAAAAAAMVM/uTZ3r8iww6M/s1600/newtree2dlowe.jpg)
You can select among various types of format such as FASTA, Genbank, and XML. I prefer to ch oose mitochondrial D-loop hypervariable region I to further multiple alignment and phylogenetic tree analysis.Īfter clicking the sequence, the web page displays as shown in the figure. Retrieving dataĬlick the nulecleotide panel as shown in the figure.įind the most relevant nucleotide sequence from database. Open the NCBI webpage and type “neanderthal” in the search box. Procedure Retrive data from NCBI database Multiple aligment Progressive-pairwise method Clustalw or clustalx Phylogenetic tree analysis Bootstraping Distance matrix Neighborhood joining method Find out the consense tree from previous bootstrapped tree data Assignment 3 Phylogenetic tree Yaikwawong Metha