PHYLIP versus PAUP?

newsmgr at merrimack.edu newsmgr at merrimack.edu
Fri Dec 5 14:10:06 EST 1997


Relay-Version: ANU News - V6.2.0 06/23/97 OpenVMS AXP V6.2; site chasm
Path: chasm!cam-news-feed2.bbnplanet.com!cam-news-hub1.bbnplanet.com!news.b=
bnplanet.com!news.idt.net!newsfeed.internetmci.com!152.163.199.19!portc03.b=
lue.aol.com!audrey01.news.aol.com!not-for-mail
Newsgroups: bionet.molbio.evolution
Subject: Re: PHYLIP versus PAUP?
Message-ID: <19971205164801.LAA25374 at ladder01.news.aol.com>
From: foxik at aol.com (Foxik)
Date: 5 Dec 1997 16:48:14 GMT
References: <666rq5$s71 at net.bio.net>
Organization: AOL http://www.aol.com
Lines: 138
NNTP-Posting-Host: ladder01.news.aol.com
X-Admin: news at aol.com
Mime-Version: 1.0
Content-Type: text/plain; charset=3DISO-8859-1
Content-Transfer-Encoding: 8bit

Dr. Felsenstein,
Thank you very much for your reply. I still think that I have a very big ga=
p in
my unrooted trees education.

<<This is a matter of what your eyeball tells you.  If you unroot the tree
that is in DRAWGRAM, you get the tree in DRAWTREE.  If you assume that the
root in DRAWGRAM means something, when it doesn't, you will be kidding
yourself.>>

Here is a real life example of the same data displayed as consensus tree (u=
pper
tree), unrooted tree (middle tree), and a tree rooted at midpoint (lower tr=
ee).
Hope the format will hold on a post-board. The trees were produced with the
GCG-PAUP. PHYLIP is giving very similar results, but it was easier for me t=
o do
file manipulations in PAUP. Well my eyeball tells me that consensus and
unrooted tree are identical twins. On the other hand the rooted tree althou=
gh
recognizable as a child of the same parents has significant differences. I
don=92t have problems with cluster-A. I can very well see this cluster on b=
oth
types of trees and I am assuming that it is separated from clusters B and C=
 by
91% (is that correct?). Cluster B is separated from cluster D by 97%, but f=
rom
cluster C (consist of only one species) by 67% (that means that it is not
actually separated). Cluster DC is separated from everything else by 86% an=
d C
and D are one cluster (separation only by 51%).

Well, everything looks good when you don=92t know what the species are. The
problem is that species 1 through 15 are very closely related to each other=
=2E
Species 16 is the one which stands alone by all type of comparisons includi=
ng
rooted trees. But I cannot see that this in the case in the unrooted trees.=
 It
is beyond my comprehension how the most different species in the whole set =
of
data does not look different in unrooted trees. May be I am not reading tho=
se
unrooted trees correctly. In that case could somebody explain to me what
bootstrap value I can put on a fork which separate species 16 from all othe=
r
species in the rooted (lower) tree. And, Oh boy, it must be the most
significant statistical separation. I would greatly appreciate if somebody =
can
educate how to read these unrooted and consensus trees.

Bootstrap 50% majority-rule consensus tree

/---------------------------------------------------------------  (1)
|
+---------------------------------------------------------------  (2)   A=
=20
|
|                                                     /---------  (3)     =
=20
|        /---------------------52---------------------+
|        |                                            \---------  (4)
|        |
|        |                                   /------------------  (5)
|        |                                   |
|        |                                   |        /---------  (6)   B
|        |                          /---98---+---55---+
\---67---+                          |        |        \---------  (7)
         |                          |        |
         |        /-------97--------+        \------------------  (8)
         |        |                 |
         |        |                 \---------------------------  (9)
         |        |
         |        |        /------------------------------------  (10) C
         \---91---+        |
                  |        |                          /---------  (11)
                  |        |                 /---72---+
                  |        |                 |        \---------  (12)
                  \---64---+                 |
                           |                 +------------------  (13) D
                           |        /---51---+
                           |        |        +------------------  (14)
                           |        |        |
                           \---86---+        \------------------  (16)
                                    |
                                    \---------------------------  (15)
 =20
                                       =20
Unrooted tree  =20
/------------------------------------------------------------------- (1)
|
+------------------------------------------------------------------- (2)
|
|                                                        /---------- (3)
|         /---------------------------------------------17
27        |                                              \---------- (4)
|         |
|         |                                     /------------------- (5)
|         |                                     |
|         |                                     |        /---------- (6)
|         |                           /--------19-------18
\--------26                           |         |        \---------- (7)
          |                           |         |
          |        /-----------------20         \------------------- (8)   =
   =20
  |        |                  |
          |        |                  \----------------------------- (9)
          |        |
          |        |         /-------------------------------------- (10)
          \-------25         |
                   |         |                           /---------- (11)
                   |         |                  /-------21
                   |         |                  |        \---------- (12)
                   \--------24                  |
                             |                  +------------------- (13)
                             |        /--------22
                             |        |         +------------------- (14)
                             |        |         |
                             \-------23         \------------------- (16)
                                      |
                                      \----------------------------- (15)
  =20
                                                      =20
Rooted at midpoint

                                                           /-------- (1)
                                                  /-------27
                                                  |        \-------- (2)
                                 /---------------26
                                 |                |        /-------- (3)
                                 |                \-------17
                                 |                         \-------- (4)
                                 |
                                 |                /----------------- (5)
                         /------25                |
                         |       |                |        /-------- (6)
                         |       |        /------19-------18
                         |       |        |       |        \-------- (7)
                         |       |        |       |
                 /------24       \-------20       \----------------- (8)
                 |       |                |
                 |       |                \------------------------- (9)
        /-------23       |
        |        |       \------------------------------------------ (10)
        |        |
        |        \-------------------------------------------------- (15)
        |
        |                                                  /-------- (11)
/------22-------------------------------------------------21
|       |                                                  \-------- (12)
|       |
|       +----------------------------------------------------------- (13)
|       |
|       \----------------------------------------------------------- (14)
|
\------------------------------------------------------------------- (16)
                                                      =20




More information about the Mol-evol mailing list