/usr/share/doc/phylip/README.Debian is in phylip 1:3.696+dfsg-5.
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Because Phylip is made of several different programs, some of
which having names which conflict with other Unix programs
(like "factor"), the Debian installation uses a wrapper,
named "phylip", which is used to invoke the specific programs.
So, to run dnapenny, you type:
phylip dnapenny
If it bothers you, just add "/usr/lib/phylip/bin" in front of
your PATH and you'll get the Phylip programs as usual.
Test files and samples are in /usr/share/doc/phylip/examples/tests.
Just type make.
The reference Web site is:
http://evolution.genetics.washington.edu/phylip.html
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