The question is...
How bioinformatics tools can be use to prove that Neanderthal is close to modern human than other apes, namely, gorillas, chimpanzees, bonobos, siamangs, orangutans, and gibbons.

The bioinformatics tools, which used to create the phygenetic tree consist of ClustalX, Phylip(package), and TreeView32.

From the well established data show that mitochodrial D-loop sequence is a certain region found in neanderthal genome,therefore I choose and retrive the sequences of D-loop region of 8 species from the NCBI data base and the accession numbers are as follows, Homo sapiens neanderthalensis AF254446 for Neanderthal, Homo sapiens S80333 for Modern human, Pan paniscus NC001644 for Bonobos, Pan troglodytes NC00164 for Chimpanzees, Gorilla gorilla gorilla AJ812285 for Gorillas, Hylobates syndactylus AF035467 for Gibbons , Pongo pygmaeus NC001646 for Orangutans, and Symphalangus syndactylus DQ 862113 for Siamangs then saved as in fasta format. (As show in next page Click )

Step:1 Use ClustalX V1.83 for do complete alignment and export file in form of phylip format

First , loaded mitochondrail D-loop to Clustal X

click "out put fomat options" then choose export in Phylip format and Do complete alignment .

Step:2 Use Phylip Package V 3.66

- Seqboost to generate a bootstrap set of resample acording to boost straping number.
- DNAdist to calculated distance matrix from nucleotide sequence and also compute a table of similarity between the nucleotide sequence.
- Neighbor to estimate phylogenies from distance matrix by the Neighbor-joining medthod.
- Consense to compute consensus tree from bootstraped tree data.

Do following this step: seqboot >> dnadist >> neighbor >> consense >> treev32

(details of each step are in text book)

Step:3(Last step) Used the treev32 to view the outtree,after we got the outtree file from consense.exe.

You can see outtree in unrooted Tree, Cardogram, and Phylogram from treeview.

Unrooted Tree
(illustrate the relatedness of the leaf nodes without making assumptions about ancestry)

 

Cardogram
(represents a branching pattern,its branch lengths do not represent time.)

Phylogram
(explicitly represents number of character changes through its branch lengths.)

These pictures shown that the neanderthal is closed to modern human than other apes.