File phylip_documentation_path_fix.patch of Package phylip

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File phylip_documentation_path_fix.patch of Package phylip (Revision e2151b1a41355f1bb98fcac7cfb00976)

Currently displaying revision e2151b1a41355f1bb98fcac7cfb00976 , Show latest

--- phylip.html	2012-11-15 22:41:53.024754601 -0600
+++ phylip.html_new	2012-11-15 22:42:50.473726103 -0600
@@ -22,7 +22,7 @@
 documentation files for each program, in the form of web pages in HTML 3.2.
 There are also documentation web pages for each group of programs, and a
 main documentation file that is the basic introduction to the package.
-Before running any of the programs you should <A HREF="doc/main.html">read it</A>.
+Before running any of the programs you should <A HREF="main.html">read it</A>.
 
 Below you will find a list of the programs and the documentation files.
 The names of the documentation files are highlighted as links that will
@@ -32,73 +32,73 @@
 <H2>Introduction to PHYLIP</H2>
 
 <TABLE BORDER=5>
-<TR><TD><A HREF="doc/main.html">main documentation file</A></TD></TR>
+<TR><TD><A HREF="main.html">main documentation file</A></TD></TR>
 </TABLE>
 
 <H2>Molecular sequence methods</H2>
 
 <TABLE BORDER=5>
-<TR><TD></TD><TD><A HREF="doc/sequence.html">molecular sequence programs documentation file</A></TD></TR>
-<TR><TD><TT>protpars</TT></TD><TD><A HREF="doc/protpars.html">protein parsimony documentation file</A></TD></TR>
-<TR><TD><TT>dnapars</TT></TD><TD><A HREF="doc/dnapars.html">DNA sequence parsimony documentation file</A></TD></TR>
-<TR><TD><TT>dnapenny</TT></TD><TD><A HREF="doc/dnapenny.html">DNA parsimony branch and bound documentation file</A></TD></TR>
-<TR><TD><TT>dnamove</TT></TD><TD><A HREF="doc/dnamove.html">interactive DNA parsimony documentation file</A></TD></TR>
-<TR><TD><TT>dnacomp</TT></TD><TD><A HREF="doc/dnacomp.html">DNA compatibility documentation file</A></TD></TR>
-<TR><TD><TT>dnaml</TT></TD><TD><A HREF="doc/dnaml.html">DNA maximum likelihood documentation file</A></TD></TR>
-<TR><TD><TT>dnamlk</TT></TD><TD><A HREF="doc/dnamlk.html">DNA maximum likelihood with clock documentation file</A></TD></TR>
-<TR><TD><TT>proml</TT></TD><TD><A HREF="doc/proml.html">Protein sequence maximum likelihood documentation file</A></TD></TR>
-<TR><TD><TT>promlk</TT></TD><TD><A HREF="doc/promlk.html">Protein sequence maximum likelihood with clock documentation file</A></TD></TR>
-<TR><TD><TT>dnainvar</TT></TD><TD><A HREF="doc/dnainvar.html">DNA invariants documentation file</A></TD></TR>
-<TR><TD><TT>dnadist</TT></TD><TD><A HREF="doc/dnadist.html">DNA distance documentation file</A></TD></TR>
-<TR><TD><TT>protdist</TT></TD><TD><A HREF="doc/protdist.html">Protein sequence distance documentation file</A></TD></TR>
-<TR><TD><TT>restdist</TT></TD><TD><A HREF="doc/restdist.html">Restriction sites and fragments distances documentation file</A></TD></TR>
-<TR><TD><TT>restml</TT></TD><TD><A HREF="doc/restml.html">Restriction sites maximum likelihood documentation file</A></TD></TR>
-<TR><TD><TT>seqboot</TT></TD><TD><A HREF="doc/seqboot.html">Bootstrapping/Jackknifing documentation file</A></TD></TR>
+<TR><TD></TD><TD><A HREF="sequence.html">molecular sequence programs documentation file</A></TD></TR>
+<TR><TD><TT>protpars</TT></TD><TD><A HREF="protpars.html">protein parsimony documentation file</A></TD></TR>
+<TR><TD><TT>dnapars</TT></TD><TD><A HREF="dnapars.html">DNA sequence parsimony documentation file</A></TD></TR>
+<TR><TD><TT>dnapenny</TT></TD><TD><A HREF="dnapenny.html">DNA parsimony branch and bound documentation file</A></TD></TR>
+<TR><TD><TT>dnamove</TT></TD><TD><A HREF="dnamove.html">interactive DNA parsimony documentation file</A></TD></TR>
+<TR><TD><TT>dnacomp</TT></TD><TD><A HREF="dnacomp.html">DNA compatibility documentation file</A></TD></TR>
+<TR><TD><TT>dnaml</TT></TD><TD><A HREF="dnaml.html">DNA maximum likelihood documentation file</A></TD></TR>
+<TR><TD><TT>dnamlk</TT></TD><TD><A HREF="dnamlk.html">DNA maximum likelihood with clock documentation file</A></TD></TR>
+<TR><TD><TT>proml</TT></TD><TD><A HREF="proml.html">Protein sequence maximum likelihood documentation file</A></TD></TR>
+<TR><TD><TT>promlk</TT></TD><TD><A HREF="promlk.html">Protein sequence maximum likelihood with clock documentation file</A></TD></TR>
+<TR><TD><TT>dnainvar</TT></TD><TD><A HREF="dnainvar.html">DNA invariants documentation file</A></TD></TR>
+<TR><TD><TT>dnadist</TT></TD><TD><A HREF="dnadist.html">DNA distance documentation file</A></TD></TR>
+<TR><TD><TT>protdist</TT></TD><TD><A HREF="protdist.html">Protein sequence distance documentation file</A></TD></TR>
+<TR><TD><TT>restdist</TT></TD><TD><A HREF="restdist.html">Restriction sites and fragments distances documentation file</A></TD></TR>
+<TR><TD><TT>restml</TT></TD><TD><A HREF="restml.html">Restriction sites maximum likelihood documentation file</A></TD></TR>
+<TR><TD><TT>seqboot</TT></TD><TD><A HREF="seqboot.html">Bootstrapping/Jackknifing documentation file</A></TD></TR>
 </TABLE>
 
 <H2>Distance matrix methods</H2>
 
 <TABLE BORDER=5>
-<TR><TD></TD><TD><A HREF="doc/distance.html">Distance matrix programs documentation file</A></TD></TR>
-<TR><TD><TT>fitch</TT></TD><TD><A HREF="doc/fitch.html">Fitch-Margoliash distance matrix method documentation file</A></TD></TR>
-<TR><TD><TT>kitsch</TT></TD><TD><A HREF="doc/kitsch.html">Fitch-Margoliash distance matrix with clock documentation file</A></TD></TR>
-<TR><TD><TT>neighbor</TT></TD><TD><A HREF="doc/neighbor.html">Neighbor-Joining and UPGMA method documentation file</A></TD></TR>
+<TR><TD></TD><TD><A HREF="distance.html">Distance matrix programs documentation file</A></TD></TR>
+<TR><TD><TT>fitch</TT></TD><TD><A HREF="fitch.html">Fitch-Margoliash distance matrix method documentation file</A></TD></TR>
+<TR><TD><TT>kitsch</TT></TD><TD><A HREF="kitsch.html">Fitch-Margoliash distance matrix with clock documentation file</A></TD></TR>
+<TR><TD><TT>neighbor</TT></TD><TD><A HREF="neighbor.html">Neighbor-Joining and UPGMA method documentation file</A></TD></TR>
 </TABLE>
 
 <H2>Gene frequencies and continuous characters</H2>
 
 <TABLE BORDER=5>
-<TR><TD></TD><TD><A HREF="doc/contchar.html">Continuous characters and gene frequencies documentation file</A></TD></TR>
-<TR><TD><TT>contml</TT></TD><TD><A HREF="doc/contml.html">Maximum likelihood continuous characters and gene frequencies documentation file</A></TD></TR>
-<TR><TD><TT>contrast</TT></TD><TD><A HREF="doc/contrast.html">Contrast method documentation file</A></TD></TR>
-<TR><TD><TT>gendist</TT></TD><TD><A HREF="doc/gendist.html">Genetic distance documentation file</A></TD></TR>
+<TR><TD></TD><TD><A HREF="contchar.html">Continuous characters and gene frequencies documentation file</A></TD></TR>
+<TR><TD><TT>contml</TT></TD><TD><A HREF="contml.html">Maximum likelihood continuous characters and gene frequencies documentation file</A></TD></TR>
+<TR><TD><TT>contrast</TT></TD><TD><A HREF="contrast.html">Contrast method documentation file</A></TD></TR>
+<TR><TD><TT>gendist</TT></TD><TD><A HREF="gendist.html">Genetic distance documentation file</A></TD></TR>
 </TABLE>
 
 <H2>Discrete characters methods</H2>
 
 <TABLE BORDER=5>
-<TR><TD></TD><TD><A HREF="doc/discrete.html">Discrete characters methods documentation file</A></TD></TR>
-<TR><TD><TT>pars</TT></TD><TD><A HREF="doc/pars.html">Unordered multistate parsimony documentation file</A></TD></TR>
-<TR><TD><TT>mix</TT></TD><TD><A HREF="doc/mix.html">Mixed method parsimony documentation file</A></TD></TR>
-<TR><TD><TT>penny</TT></TD><TD><A HREF="doc/penny.html">Branch and bound mixed method parsimony documentation file</A></TD></TR>
-<TR><TD><TT>move</TT></TD><TD><A HREF="doc/move.html">Interactive mixed method parsimony documentation file</A></TD></TR>
-<TR><TD><TT>dollop</TT></TD><TD><A HREF="doc/dollop.html">Dollo and polymorphism parsimony documentation file</A></TD></TR>
-<TR><TD><TT>dolpenny</TT></TD><TD><A HREF="doc/dolpenny.html">Dollo and polymorphism branch and bound parsimony documentation file</A></TD></TR>
-<TR><TD><TT>dolmove</TT></TD><TD><A HREF="doc/dolmove.html">Dollo and polymorphism interactive parsimony documentation file</A></TD></TR>
-<TR><TD><TT>clique</TT></TD><TD><A HREF="doc/clique.html">0/1 characters compatibility method documentation file</A></TD></TR>
-<TR><TD><TT>factor</TT></TD><TD><A HREF="doc/factor.html">Character recoding program documentation file</A></TD></TR>
+<TR><TD></TD><TD><A HREF="discrete.html">Discrete characters methods documentation file</A></TD></TR>
+<TR><TD><TT>pars</TT></TD><TD><A HREF="pars.html">Unordered multistate parsimony documentation file</A></TD></TR>
+<TR><TD><TT>mix</TT></TD><TD><A HREF="mix.html">Mixed method parsimony documentation file</A></TD></TR>
+<TR><TD><TT>penny</TT></TD><TD><A HREF="penny.html">Branch and bound mixed method parsimony documentation file</A></TD></TR>
+<TR><TD><TT>move</TT></TD><TD><A HREF="move.html">Interactive mixed method parsimony documentation file</A></TD></TR>
+<TR><TD><TT>dollop</TT></TD><TD><A HREF="dollop.html">Dollo and polymorphism parsimony documentation file</A></TD></TR>
+<TR><TD><TT>dolpenny</TT></TD><TD><A HREF="dolpenny.html">Dollo and polymorphism branch and bound parsimony documentation file</A></TD></TR>
+<TR><TD><TT>dolmove</TT></TD><TD><A HREF="dolmove.html">Dollo and polymorphism interactive parsimony documentation file</A></TD></TR>
+<TR><TD><TT>clique</TT></TD><TD><A HREF="clique.html">0/1 characters compatibility method documentation file</A></TD></TR>
+<TR><TD><TT>factor</TT></TD><TD><A HREF="factor.html">Character recoding program documentation file</A></TD></TR>
 </TABLE>
 
 <H2>Tree drawing, consensus, tree editing, tree distances</H2>
 
 <TABLE BORDER=5>
-<TR><TD></TD><TD><A HREF="doc/draw.html">Tree drawing programs documentation file</A></TD></TR>
-<TR><TD><TT>drawgram</TT></TD><TD><A HREF="doc/drawgram.html">Rooted tree drawing program documentation file</A></TD></TR>
-<TR><TD><TT>drawtree</TT></TD><TD><A HREF="doc/drawtree.html">Unrooted tree drawing program documentation file</A></TD></TR>
+<TR><TD></TD><TD><A HREF="draw.html">Tree drawing programs documentation file</A></TD></TR>
+<TR><TD><TT>drawgram</TT></TD><TD><A HREF="drawgram.html">Rooted tree drawing program documentation file</A></TD></TR>
+<TR><TD><TT>drawtree</TT></TD><TD><A HREF="drawtree.html">Unrooted tree drawing program documentation file</A></TD></TR>
 <TR><TD>&nbsp;</TD><TD>&nbsp;</TD></TR>
-<TR><TD><TT>consense</TT></TD><TD><A HREF="doc/consense.html">Consensus tree program documentation file</A></TD></TR>
-<TR><TD><TT>treedist</TT></TD><TD><A HREF="doc/treedist.html">Tree distance program documentation file</A></TD></TR>
-<TR><TD><TT>retree</TT></TD><TD><A HREF="doc/retree.html">interactive tree rearrangement program documentation file</A></TD></TR>
+<TR><TD><TT>consense</TT></TD><TD><A HREF="consense.html">Consensus tree program documentation file</A></TD></TR>
+<TR><TD><TT>treedist</TT></TD><TD><A HREF="treedist.html">Tree distance program documentation file</A></TD></TR>
+<TR><TD><TT>retree</TT></TD><TD><A HREF="retree.html">interactive tree rearrangement program documentation file</A></TD></TR>
 </TABLE>
 </DIV>
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File phylip_documentation_path_fix.patch of Package phylip (Revision e2151b1a41355f1bb98fcac7cfb00976)

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