The Options Menu
The menu is straightforward. It typically looks like this (this one isfor DNAPARS):
DNA parsimony algorithm, version 3.5c Setting for this run: U Search for best tree? Yes J Randomize input order of sequences? No. Use input order O Outgroup root? No, use as outgroup species 1 T Use Threshold parsimony? No, use ordinary parsimony M Analyze multiple data sets? No I Input sequences interleaved? Yes 0 Terminal type (IBM PC, VT52, ANSI)? ANSI 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Print out steps in each site No 5 Print sequences at all nodes of tree No 6 Write out trees onto tree file? Yes Are these settings correct? (type Y or the letter for one to change)If you want to accept the default settings (they are shown in the above case) you can simply type "Y" followed by a carriage-return (Enter) character. If you want to change any of the options, you should type the letter shown to the left of its entry in the menu. For example, to set a threshold type "T". Lower-case letters will also work. For many of the options the program will ask for supplementary information, such as the value of the threshold.
Note the "Terminal type" entry, which you will find on all menus. It allows you to specify which type of terminal your screen is. The options are an IBM PC screen, an ANSI standard terminal (such as a DEC VT100), a DEC VT52- compatible terminal, such as a Zenith Z29, or no terminal type. Choosing "0" toggles among these four options in cyclical order, changing each time the "0" option is chosen. If one of them is right for your terminal the screen will be cleared before the menu is displayed. If none works the "none" option should probably be chosen. Keep in mind that VT-52 compatible terminals can freeze up if they receive the screen-clearing commands for the ANSI standard terminal! If this is a problem it may be helpful to recompile the program, setting the constants near its beginning so that the program starts up with the VT52 option set.
The other numbered options control which information the program will display on your screen or on the output files. The option to "Print indications of progress of run" will show information such as the names of the species as they are successively added to the tree, and the progress of global rearrangements. You will usually want to see these as reassurance that the program is running and to help you estimate how long it will take. But if you are running the program "in background" as can be done on multitasking and multiuser systems such as Unix, and do not have the program running in its own window, you may want to turn this option off so that it does not disturb your use of the computer while the program is running.
The exact contents of the output file vary from program to program and
also depend on which menu options you have selected. For many programs, if you
select all possible output information, the output will consist of (1) the name
of the program and its version number, (2) the input information printed out,
(3) a series of phylogenies, some with associated information indicating how
much change there was in each character or on each part of the tree. A typical
rooted tree looks like this:
The Output File
Most of the programs write their output onto a file called (usually)
"outfile", and a representation of the trees found onto a file called
"treefile".
+-------------------Gibbon
+----------------------------2
! ! +------------------Orang
! +------4
! ! +---------Gorilla
+-----3 +--6
! ! ! +---------Chimp
! ! +----5
--1 ! +-----Human
! !
! +-----------------------------------------------Mouse
!
+------------------------------------------------Bovine
The interpretation of the tree is fairly straightforward: it "grows" from left
to right. The numbers at the forks are arbitrary and are used (if present)
merely to identify the forks. In some of the programs asterisks ("*") are used
instead of numbers. For many of the programs the tree produced is unrooted.
It is printed out in nearly the same form, but with a warning message:
remember: this is an unrooted tree!
The warning message ("remember: ...") indicates that this is an unrooted tree
(mathematicians still call this a tree, though some systematists unfortunately
use the term "network". This conflicts with standard mathematical usage, which
reserves the name "network" for a completely different kind of graph). The
root of this tree could be anywhere, say on the line leading immediately to
Mouse. As an exercise, see if you can tell whether the following tree is or is
not a different one from the above:
+-----------------------------------------------Mouse
!
+---------4 +------------------Orang
! ! +------3
! ! ! ! +---------Chimp
---6 +----------------------------1 ! +----2
! ! +--5 +-----Human
! ! !
! ! +---------Gorilla
! !
! +-------------------Gibbon
!
+-------------------------------------------Bovine
remember: this is an unrooted tree!
(it is NOT different). It is IMPORTANT also to realize that the lengths of the
segments of the printed tree may not be significant: some may actually
represent branches of zero length, in the sense that there is no evidence that
the branches are nonzero in length. Some of the diagrams of trees attempt to
print branches approximately proportional to estimated branch lengths, while in
others the lengths are purely conventional and are presented just to make the
topology visible. You will have to look closely at the documentation that
accompanies each program to see what it presents and what is known about the
lengths of the branches on the tree. The above tree attempts to represent
branch lengths approximately in the diagram. But even in those cases, some of
the smaller branches are likely to be artificially lengthened to make the tree
topology clearer. Here is what a tree from DNAPARS looks like, when no attempt
is made to make the lengths of branches in the diagram proportional to
estimated branch lengths:
+--Human
+--5
+--4 +--Chimp
! !
+--3 +-----Gorilla
! !
+--2 +--------Orang
! !
+--1 +-----------Gibbon
! !
--6 +--------------Mouse
!
+-----------------Bovine
remember: this is an unrooted tree!
Some of the parsimony programs in the package can print out a table of the
number of steps that different characters (or sites) require on the tree. This
table may not be obvious at first. A typical example looks like this:
steps in each site:
0 1 2 3 4 5 6 7 8 9
*-----------------------------------------
0! 2 2 2 2 1 1 2 2 1
10! 1 2 3 1 1 1 1 1 1 2
20! 1 2 2 1 2 2 1 1 1 2
30! 1 2 1 1 1 2 1 3 1 1
40! 1
The numbers across the top and down the side indicate which site is being
referred to. Thus site 23 is column "3" of row "20" and has 2 steps in this
case.
The Tree File
In output from most programs, a representation of the tree is also written
into the tree file (usually named "treefile"). The tree is specified by the
nested pairs of parentheses, enclosing names and separated by commas. If there
are any blanks in the names, these must be replaced by the underscore character
"_". Trailing blanks in the name may be omitted. The pattern of the
parentheses indicates the pattern of the tree by having each pair of
parentheses enclose all the members of a monophyletic group. The tree file for
the above tree would have its first line look like this:
((Mouse,Bovine),((Orang,(Gorilla,(Chimp,Human))),Gibbon));
In the above tree the first fork separates the lineage leading to Mouse and
Bovine from the lineage leading to the rest. Within the latter group there is
a fork separating Gibbon from the rest, and so on. The entire tree is enclosed
in an outermost pair of parentheses. The tree ends with a semicolon. In some
programs such as DNAML, FITCH, and CONTML, the tree will be completely unrooted
and specified by a bottommost fork with a three-way split, with three "monophyletic" groups separated by two commas:
(A,(B,(C,D)),(E,F));The three "monophyletic" groups here are A, (B,C,D), and (E,F). The single three-way split corresponds to one of the interior nodes of the unrooted tree (it can be any interior node). The remaining forks are encountered as you move out from that first node, and each then appears as a two-way split. You should check the documentation files for the particular programs you are using to see in which of these forms you can expect the user tree to be in. Note that many of the programs that estimate an unrooted tree produce trees in the treefile in rooted form! This is done for reasons of arbitrary internal bookkeeping. The placement of the root is arbitrary.
For programs estimating branch lengths, these are given in the trees in the tree file as real numbers following a colon, and placed immediately after the group descended from that branch. Here is a typical tree with branch lengths:
((cat:47.14069,(weasel:18.87953,((dog:25.46154,(raccoon:19.19959, bear:6.80041):0.84600):3.87382,(sea_lion:11.99700, seal:12.00300):7.52973):2.09461):20.59201):25.0,monkey:75.85931);Note that the tree may continue to a new line at any time except in the middle of a name or the middle of a branch length, although in trees written to the tree file this will only be done after a comma.
These representations of trees are a subset of the standard adopted on June 24, 1986 at the annual meetings of the Society for the Study of Evolution at an meeting (the final session in a local lobster restaurant) of an informal committee consisting of Wayne Maddison (MacClade), David Swofford (PAUP), F. James Rohlf (NTSYS-PC), Chris Meacham (COMPROB and plotting programs), James Archie (character coding program), William H.E. Day, and me. This standard is a generalization of PHYLIP's format, itself based on a well-known representation of trees in terms of parenthesis patterns which has been around for almost a century. The standard is now employed by most phylogeny computer programs but unfortunately has yet to be decribed in a formal published description.
Back to the main PHYLIP page
Back to the SEQNET home page
Maintained 15 Jul 1996 -- by Martin Hilbers(e-mail:M.P.Hilbers@dl.ac.uk)