PHYLOGENETIC ANALYSIS USING DISTANCE METHODS
Oct. 15, 2014
PHYLIP Main documentation: $doc/Phylip/main.html
PHYLIP Distance methods: $doc/Phylip/distance.html
PHYLIP DNADIST: $doc/Phylip/dnadist.html
PHYLIP PROTDIST: $doc/Phylip/protdist.html
PHYLIP FITCH: $doc/Phylip/fitch.html
PHYLIP PROTDIST: $doc/Phylip/kitsch.html
PHYLIP NEIGHBOR: $doc/Phylip/neighbor.html
ATV tree viewer: $doc/atv/atv_documentation.pdf
|The PHYLIP programs are command line programs, but
can be run by BioLegato.
The programs in the PHYLIP package are interactive
programs designed to be run at the command line. BioLegato
can run these programs by generating the keystrokes you
would have typed to set program parameters.
Construction of a phylogeny using distance methods
involves two steps:
- blnalign and blpalign run DNADIST and PROTDIST,
respectively, to construct a distance matrix.
- The distance matrix is used to construct a
phylogenetic tree, using any of a number of methods
implemented in the programs FITCH, KITSCH or NEIGHBOR.
Example: Plant Type III Chitinases
The chitinases in plants are hydrolytic enzymes that degrade chitins
(N-acetyl glucosamine). Although chitin does not occur in
plants, in many fungi, it is a major component of the fungal
cell wall. Not surprisingly, chitinases are produced in plants in
response to fungi. Chitinases have been demonstrated to play an
important role in plant defense responses. There are six classes of
chitinases so far identified. Most known chitinases fall into the
Type I and Type II classes. This exercise will work with a smaller
class of genes encoding Type III chitinases.
1. The dataset
The file chitIII.mrtrans.gde is a
GDE format file containing protein coding sequences (CDS) from
chitinase III genes. These DNA sequences have already been aligned
using Pearson's mrtrans program, which reads a set of unaligned DNA
sequences and aligns them according to a set of aligned proteins.
Create a directory called distance, and save chitIII.mrtrans.gde
to this directory. Open the file in blnalign:
2. A quick phylogeny using FITCH
For routine distance tree construction, the
method of Fitch and Margoliash is the method of choice. FITCH
allows for variable rates of evolution in different lineages, and
iterates the tree to minimize the least squares distance across
the entire tree. Although Neighbor-Joining is faster, it is also
much less thorough, considering one tree. It is probably the least
rigorous method for constructing a phylogeny . To run FITCH,
choose Phylogeny --> DNA Distance methods. Fitch-Margoliash
is the default method.
DNADIST will calculate a distance matrix, and then FITCH will
run, and by default, 3 windows will appear.
report on the phylogeny
- the machine -readable treefile. Readable by programs such as
DRAWTREE, DRAWGRAM, and ATV.
The treefile also pops up on a bltree window, allowing further
tasks to be performed using the tree as input.
TREEFILE - the treefile in the ATV tree editor.
|Hint: Each of these files need to be saved separately,
if you wish to save them. Give them all the same base
name, but different extensions, such as
Note: Do NOT save the contents of the ATV window using
the .treefile extension. You will overwrite the original
treefile. ATV can save files in NHX (New Hampshire,
extended) format, which will preserve any changes
made in ATV. In most cases, you can just save the
.treefile and read it into ATV, treetool, or other
tree drawing programs whenever you want to work with it.
3. Phylogeny using amino acid sequences.
Since also possible to construct distance matricies for multiple
alignments of amino acid sequences, the same programs (FITCH,
KITSCH, and NEIGHBOR) can be used to construct distance trees. The
contains the chitinase III proteins aligned using TCOFFEE. Open this
file with blpalign.
Some of the parameters for construction of the distance matrix using
PROTDIST are different from those for DNADIST. These include
several different methods for constructing distance matrices, as
well as a choice of alternative genetic codes, where appropriate.
Once the distance matrix is constructed, there is no difference in
computation of the phylogenetic tree, so all parameters are the same
FITCH will produce an outfile (chitIII.pro.fitch.outfile)
and a treefile (chitIII.pro.fitch.treefile)
similar to those with the DNA alignment. For comparison, the
treefile is shown in ATV below:
While this may look like a different tree than that produced using
the DNA alignment, the topologies (ie. the order of branching) are
identical. To prove this, we can choose the "Swap children" option
in ATV, and then click on internal nodes to rotate the branches.
Comparison with the tree from the DNA alignment shows that these
trees have identical topologies, and similar lengths for most