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190
PAUP 3.1 USER'S MANUAL
[NO]INDICES
Specify INDICES to request calculation of a variety of consensus
indices. The indices computed by PAUP are described in Rohlf (1982)
and Swofford (1991) .
[NO]SAVE
If SAVE is specified, a description of all consensus trees computed
is output to a file containing a NEXUS-format TREES block. This
option is not persistent; you must specify it on every CONTREE
command for which you want a tree file to be saved.
The following options apply only if SAVE is specified.
FILE = file-specification
Specifies the name for the tree file. If file-specification
contains any of the characters equal-sign (=), semicolon (;),
colon (:), or blank, it must be enclosed within singlequotes.
{ REPLACE | APPEND }
Ordinarily, if SAVE is requested and the specified file (see
FILE option above) already exists, you will be prompted
for confirmation that the existing file should be replaced.
Explicit specification of REPLACE suppresses this prompt;
the existing file will be quietly overwritten by the new data.
Alternatively, you may specify APPEND, in which case a
new TREES block will be concatenated to the end of an
existing file. The APPEND option is mainly useful only
for archival purposes, as current versions of PAUP and
MacClade can process only the first TREES block in a file.
For obvious reasons, this option is not persistent.
ROOT = { OUTGROUP | LUNDBERG | MIDPOINT }
OUTROOT = { POLYTOMY | PARAPHYL | MONOPHYL }
[NO]TCOMPRESS
See "Options Affecting Multiple Commands" earlier in this
chapter.