Neighbor Joining method in Phylip

To carry out phylogenetic analysis it is important to begin with an alignment in which all gap-containing positions have been removed.

• This can be accomplished using the gap strip tool.

• There is a bug in the process but the gap-free alignment can be loaded into clustalX, the the save sequences as "Phylip" format function can be used.

• The correct alignment can be created with a text editor. Another version of it is in your clustal/phylip folder called tiny_nogap.phy

• enter the phylip folder:

• The first step to to create the bootstrap replicates. This is done with the phylip application seqboot.

• when prompted, provide the name "tiny_nogap.phy".

• At the interactive menu:

  • change option r to 10 for 10 replicates. NOTE: normally the number used is 1000 for neighbor

• Move outfile to tiny_nogap.seqboot

• The next step is to calculate the distances between the sequences in each replicate. This is done with protdist

• when prompted, provide the name "tiny_nogap.seqboot".

• At the interactive menu:

  • change option m to d for datasets and 10 for number of replicates.

• Rename the outfile

• Build the neighbor-joining tree for each distance matrix wth neighbor:

• when prompted, provide the name "tiny_nogap.protdist".

• At the interactive menu:

  • change option m to 10 for number of replicates.

  • enter 111 for random number seed

• Rename the output:

• Create a consensus version of the outtree file with consense:

• when prompted, provide the name "tiny_nogap.neightree".

• At the interactive menu, default settings are ok so type "Y"

• Rename the output:

• Draw the tree with drawtree:

• when prompted for a file enter tiny_nogap.neigh.constree

• when prompted for a fontfile, enter:

• At the interactive menu, select option V, then N to turn off preview. Then option Y

• This results in a postscript plot of the tree. rename it to:

• The contents of this file can be viewed with photo software like but it looks like this:

• The bootstrap values can be viewed in the file tiny_nogap.neigh.constree. Or graphicall by opening this file with . With branch lengths selected, the view looks like this: