Windows
Phylogeny Programs
Step2: Do multiple sequence alignment of the sequence of interest using ClustalX software. In clustalx software, choose 'save as phylip' option. After MSA, you will be saved three output file'.aln', '.dnd', and '.phy' files.
Note: While doing clustalx, please note that the first header lines or organism names or protein names in fasta sequence file should be unique. If same or repetive names or gap between each fasta sequences occurs then clustalx will not run properly.
Step4: Copy '.phy file in C:/Program files/Phylip/exe/ folder
Step3: In C:/Program files/Phylip/exe/ folder, open bootstrap option. Now drag and drop'
'.phy' phylip file, (calling it infile) Do 100 replicates. Give Random seed number: 3 (must be odd)
click Y to all the default parameters.
Step4. Open DnaDist (call infile, if you want, the previous outfile ) and change dataset as MULTIPLE DATASET, telling you did 100 replicates
Step5: Run neighbourjoining (call infile, if you want, the previous outfile ), and set multiple dataset to 100. you can set a root.
Now you have 100 trees in the outtree file.
you can already open this file with treeview, adding the extention .ph to the file.
Step6: Create a consensus tree: Run Consensus calling intree the outtree from NJ.
Step7. See the outtree.ph (i.e, fourth file that generated after running neighbourjoining) in Treeview.
Notes: in treeview from Tree Menu set: Internal edge label to see the bootstrap values.
The 'real tree' is the first of the 100 created by NJ, the consensus tree is useful to know how reliable are the branches and the nodes.
Cached
Phylip Software
PHYLIP version 3.6 is my own package. It is available free, from its Web site, in C source code, or as executables for Windows, Mac OS X, and Mac OS 8 or 9. The C source code can easily be compiled on Unix or Linux systems. Fortunately, the PHYLIP programs have been repackaged as part of the EMBOSS software package, which provides a much more modern command line interface around the PHYLIP programs. In addition, EMBOSS provides some other very helpful programs for producing files in the correct format. TreeView is a free phylogenetic tree viewer software for Windows. In this software, you can open and edit the evolutionary trees of different species. Hence, by analyzing the evolutionary trees, you can study how the process of evolution has taken place in different species. Using PHYLIP Software to Generate Neighbor-Joining or UPGMA Trees from Genetic or Morphological Distance Matrices Introduction: PHYLIP (created by Joe Felsenstein) is a very flexible program for conducting phylogenetic analyses from genetic or morphological data sets. It can be used for a number of different analyses. Our lab uses it.