Phylogeny From A Distance Matrix

Question

[Mara]

I created a distance matrix based on structural variation between many similar proteins and would like to use this to generate a phylogenetic tree. Does anyone know how to help me get started?

Answer 1

[Rvosa]

There's a number of commonly-used programs that you might consider, PHYLIP has programs that operate on distance matrices (http://evolution.genetics.washington.edu/phylip/doc/distance.html) and so does paup (http://paup.csit.fsu.edu/).

Answer 2

[Thaman]

This is an excellent paper where you can find all phylogeny approaches link. Moreover, PHYLIP has different methods like parsimony, distance matrix, maximum likelihood, bootstrapping and e.t.c. In your case you can use PROTDIST in particular.

Edit

We have already discussed several times here in Biostar Phylogenetic Analysis

Answer 3

[Panos]

In phylip, if you already have a distance matrix, then you just need to run "neighbor" (for neighbor-joining trees) and give your distance matrix as input (either rename it to "infile" or enter its name after you start the program). One of the output files will be "outtree". Rename this to "intree"

Then, in order to draw the tree, run "drawgram", change the settings according to what you want to get and hit "y" to draw the tree. Sometimes it complains about not finding some font. If this happens, enter "font1" as the font name when asked.

If you don't have distance matrix, "dnadist"/"protdist" programs can be used.

Hope this helps! I was doing this procedure some years ago... If there are no big changes in phylip, it should work!

[Mara]

Thank you. It's been a long time since I used Phylip and the data input files are tricky, but got it to work!

[wwjulian521]

I finally use Phylip to get the outtree, but i can't open it with Treeview, it said:"label "xxx" already exists",