EMBOSS FAQ (Frequently Asked Questions)

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available from our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/ in file PHYLIP-3.6b.tar.gz

If you have done a full installation of EMBOSS using a 'prefix' e.g. you configured with ./configure --prefix=/usr/local/emboss and followed this with a 'make install' (highly recommended) then:

1) gunzip and untar the file anywhere

       gunzip PHYLIP-3.6b.tar.gz
       tar xf PHYLIP-3.6b.tar

2) go into the phylip directory

       cd PHYLIP-3.6b

3) configure and compile

       ./configure (use same options as you used to compile emboss)
       make
       make install

       N.B. If you configured without using a prefix but did do
            a 'make install' (or specified a prefix of /usr/local,
            which amounts to the same thing) then you must configure
            using:
            ./configure --prefix=/usr/local --enable-localforce

If, on the other hand, you did not do a 'make install' of EMBOSS then:

1) Go to the emboss directory

       cd EMBOSS-3.0.0

2) make new directory embassy if it does not exist already.

       mkdir embassy

3) Go into that directory

       cd embassy

4) gunzip and untar the file

       gunzip PHYLIP-3.6b.tar.gz
       tar xvf PHYLIP-3.6b.tar

5) go into the phylip directory

       cd PHYLIP-3.6b

6) configure and compile

       ./configure (use same options as you used to compile emboss)
       make

(Continued on next part...)

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