phylogenetic analysis tools and uses...part 2

Phylogenetic programs:-

Phylogenetic tree reconstruction is not a trivial task. Although there are numerous

phylogenetic programs available, knowing the theoretical background, capabilities, and

limitations of each is very important.

 Phylip (Phylogenetic inference package; by Joe Felsenstein):-

is a free multiplatform

comprehensive package containing thirty-five subprograms for performing distance,

parsimony, and likelihood analysis, as well as bootstrapping for both nucleotide and amino 

acid sequences.

Phylip (Phylogeny Inference Package):-

Phylip (Phylogeny Inference Package) software is a free package of programs for

inferring phylogenies of living species and organisms. It is now one of the most widely used

packages for computing accurate phylogenetic trees and carrying out certain related tasks.

Joseph Felsenstein( 1980) University of Washington, has created Phylip as a free package of

programs for inferring phylogenies.

Phylip: Different useful programs

The PHYLIP programs could be classified into five categories

1- Programs for molecular sequence data (such as DNAPARS, PROTPARS, etc.);

2- Programs for distance matrix data (such as FITCH, KITSCH and NEIGHBOR);

3- Programs for gene frequencies and continuous characters (such as CONTML,

 GENDIST and CONTRAST);

4- Programs for 0-1 discrete state data (such as MIX, MOVE, CLIQUE, etc.);

5- Programs for plotting trees and consensus trees (such as DRAWTREE,

 CONSENSE,etc.).

Phylip: Advantages and disadvantages

Advantages:

1. Phylip is very easy to use and free of charge.

2. Phylip is stand-alone software that can run on any computer.

3. The recent version contains many programs for different kinds of data.

4. Some sites make running of Phylip programs available as a web server which can also

run on (almost) any computer that has access to the Internet and can return the results

online or by e-mail.

5. It works on as many computer systems such as Windows, Macintosh MacOS X,

Macintosh Mac OS and Linux.

6. Phylip contains different programs to analyze DNA and amino acid sequence data.

Disadvantages:

1. The format requirements for Phylip are rather stringent, and any deviation will

result in an error message "Unable to allocate memory" and then the program

terminates.

2. Phylip is used in a sequential way; the output from the first program is used as an

input in the next program.

Phylip: Methods and modules

1. Retrieve the nucleotide sequences form the genbank entrez page.

2. Allign these sequences by using clustalw.

3. Save the multiple sequence alignment in phylip format.

4. The aligned sequences will act as a input to the ‘phylip’program

5. Selcet the phylip program from the phylip folder just by clicking the ‘dnadist’program.

6. The ‘dnadist’ program have options for selecting the distance parameters, click on of

them, it produces the distance table for the given sequences.