updated port biology/phylip from vers 3.5 to 3.6

PR:		26146
Submitted by:	    "David A. Bader" <dbader@eece.unm.edu>

5 files changed, 110 insertions, 94 deletions

diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile
index b7ec309be6f0..9d73f51e11ab 100644
--- a/biology/phylip/Makefile
+++ b/biology/phylip/Makefile
@@ -6,10 +6,11 @@
 #
 
 PORTNAME=	phylip
-PORTVERSION=	3.5
+PORTVERSION=	3.6
 CATEGORIES=	biology
-MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/phylip/
+MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/phylip/phylip36/
 DISTNAME=	${PORTNAME}
+WRKSRC=		${WRKDIR}/${DISTNAME}/src
 EXTRACT_SUFX=	.tar.Z
 
 MAINTAINER=	dbader@eece.unm.edu
@@ -19,16 +20,18 @@ NO_WRKSUBDIR=	yes
 BINARIES=	clique consense contml contrast dnacomp dnadist dnainvar \
 		dnaml dnamlk dnamove dnapars dnapenny dolmove dollop \
 		dolpenny drawgram drawtree factor fitch gendist kitsch \
-		mix move neighbor penny protdist protpars restml retree \
-		seqboot
-DOCFILES=	README clique.doc consense.doc contchar.doc contml.doc \
-		contrast.doc discrete.doc distance.doc dnacomp.doc dnadist.doc \
-		dnainvar.doc dnaml.doc dnamlk.doc dnamove.doc dnapars.doc \
-		dnapenny.doc dollop.doc dolmove.doc dolpenny.doc draw.doc \
-		drawgram.doc drawtree.doc factor.doc fitch.doc gendist.doc \
-		kitsch.doc main.doc makeinf.doc mix.doc move.doc neighbor.doc \
-		penny.doc protdist.doc protml.doc protpars.doc restml.doc \
-		retree.doc seqboot.doc sequence.doc
+		mix move neighbor pars penny proml protdist protpars \
+		restdist restml retree seqboot treedist
+DOCFILES=	clique.html consense.html contchar.html contml.html \
+		contrast.html discrete.html distance.html dnacomp.html \
+		dnadist.html dnainvar.html dnaml.html dnamlk.html \
+		dnamove.html dnapars.html dnapenny.html dollop.html \
+		dolmove.html dolpenny.html draw.html drawgram.html \
+		drawtree.html factor.html fitch.html gendist.html \
+		kitsch.html main.html mix.html move.html neighbor.html \
+		pars.html penny.html phylip.gif proml.html protdist.html \
+		protpars.html restdist.html restml.html retree.html \
+		seqboot.html sequence.html treedist.html
 
 do-install:
 .for f in ${BINARIES}
@@ -37,7 +40,8 @@ do-install:
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
 .for f in ${DOCFILES}
-	${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/share/doc/${PORTNAME}
+	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${f} \
+	${PREFIX}/share/doc/${PORTNAME}
 .endfor
 .endif
 
diff --git a/biology/phylip/distinfo b/biology/phylip/distinfo
index 462e0c381b02..e67ac37b471f 100644
--- a/biology/phylip/distinfo
+++ b/biology/phylip/distinfo
@@ -1 +1 @@
-MD5 (phylip.tar.Z) = d437d19d82fd84c723a73b6420aae4fc
+MD5 (phylip.tar.Z) = b705658b0de0163fe87b6416c521d98c
diff --git a/biology/phylip/files/patch-aa b/biology/phylip/files/patch-aa
new file mode 100644
index 000000000000..78fbe0ed4f78
--- /dev/null
+++ b/biology/phylip/files/patch-aa
@@ -0,0 +1,11 @@
+--- Makefile.orig	Mon Mar 26 19:31:01 2001
++++ Makefile	Mon Mar 26 19:35:29 2001
+@@ -77,7 +77,7 @@
+ # and here are some possible DFLAGS statements:
+ #
+ # A minimal one
+-DFLAGS  = -DX -lX11
++DFLAGS  = -DX -I/usr/X11R6/include
+ #
+ # A basic one for debugging
+ #DFLAGS  = -g -DX -lX11
diff --git a/biology/phylip/pkg-descr b/biology/phylip/pkg-descr
index 34988635d2fb..332989387f17 100644
--- a/biology/phylip/pkg-descr
+++ b/biology/phylip/pkg-descr
@@ -1,45 +1,40 @@
-              PHYLIP - Phylogeny Inference Package (version 3.5)
+              PHYLIP - Phylogeny Inference Package (version 3.6)
 
-     This is a FREE package of programs for inferring phylogenies and  carrying
-out certain related tasks.  At present it contains 30 programs, which carry out
-different algorithms on different kinds of data.  The programs in  the  package
-are:
-      ---------- Programs for molecular sequence data ----------
-  PROTPARS  Protein parsimony          DNAPARS   Parsimony method for DNA
-  DNAMOVE   Interactive DNA parsimony  DNAPENNY  Branch and bound for DNA
-  DNACOMP   Compatibility for DNA      DNAINVAR  Phylogenetic invariants
-  DNAML     Maximum likelihood method  DNAMLK    DNA ML with molecular clock
-  DNADIST   Distances from sequences   PROTDIST  Distances from proteins
-  RESTML    ML for restriction sites   SEQBOOT   Bootstraps sequence data sets
-      ----------- Programs for distance matrix data ------------
-  FITCH     Fitch-Margoliash and least-squares methods
-  KITSCH    Fitch-Margoliash and least squares methods with evolutionary clock
-  NEIGHBOR  Neighbor-joining and UPGMA methods
-      -------- Programs for gene frequencies and continuous characters -------
-  CONTML    Maximum likelihood method  GENDIST  Computes genetic distances
-  CONTRAST  Computes contrasts and correlations for comparative method studies
-      ------------- Programs for 0-1 discrete state data -----------
-  MIX       Wagner, Camin-Sokal, and mixed parsimony criteria
-  MOVE      Interactive Wagner, C-S, mixed parsimony program
-  PENNY     Finds all most parsimonious trees by branch-and-bound
-  DOLLOP, DOLMOVE, DOLPENNY   same as preceding four programs, but for
-     the Dollo and polymorphism parsimony criteria
-  CLIQUE    Compatibility method       FACTOR    recode multistate characters
-      ---------- Programs for plotting trees and consensus trees -------
-  DRAWGRAM  Draws cladograms and phenograms on screens, plotters and printers
-  DRAWTREE  Draws unrooted phylogenies on screens, plotters and printers
-  CONSENSE  Majority-rule and strict consensus trees
-  RETREE    Reroots, changes names and branch lengths, and flips trees
+PHYLIP (the PHYLogeny Inference Package) is a package of programs for
+inferring phylogenies (evolutionary trees).  Methods that are
+available in the package include parsimony, distance matrix, and
+likelihood methods, including bootstrapping and consensus trees. Data
+types that can be handled include molecular sequences, gene
+frequencies, restriction sites, distance matrices, and 0/1 discrete
+characters.
 
-There is also an Unsupported Division  containing  two  programs,  makeinf  and
-ProtML, which were contributed by others and are maintained by their authors.
+The programs are controlled through a menu, which asks the users which
+options they want to set, and allows them to start the
+computation. The data are read into the program from a text file,
+which the user can prepare using any word processor or text editor
+(but it is important that this text file not be in the special format
+of that word processor -- it should instead be in "flat ASCII" or
+"Text Only" format). Some sequence analysis programs such as alignment
+programs can write data files in the PHYLIP format. Most of the
+programs look for the data in a file called "infile" -- if they do not
+find this file they then ask the user to type in the file name of the
+data file.
 
-The package includes extensive documentation files that provide the information
-necessary to use and modify the programs.
+Output is written onto special files with names like "outfile" and
+"treefile". Trees written onto "treefile" are in the Newick format, an
+informal standard agreed to in 1986 by authors of a number of major
+phylogeny packages.
 
-                             Joe Felsenstein
-                             joe@genetics.washington.edu
-                             Department of Genetics
-                             University of Washington
-                             Box 357360
-                             Seattle, Washington 98195-7360, U.S.A.
+PHYLIP is the most widely-distributed phylogeny package, and competes
+with PAUP to be the one responsible for the largest number of
+published trees. PHYLIP has been in distribution since 1980, and has
+over 6,000 registered users.
+
+ Joe Felsenstein
+ joe@genetics.washington.edu
+ Department of Genetics
+ University of Washington
+ Box 357360
+ Seattle, Washington 98195-7360, U.S.A.
+
+WWW: http://evolution.genetics.washington.edu/phylip.html
\ No newline at end of file
diff --git a/biology/phylip/pkg-plist b/biology/phylip/pkg-plist
index 9c26e88aa182..a31897854516 100644
--- a/biology/phylip/pkg-plist
+++ b/biology/phylip/pkg-plist
@@ -22,49 +22,55 @@ bin/kitsch
 bin/mix
 bin/move
 bin/neighbor
+bin/pars
 bin/penny
+bin/proml
 bin/protdist
 bin/protpars
+bin/restdist
 bin/restml
 bin/retree
 bin/seqboot
-share/doc/phylip/README
-share/doc/phylip/clique.doc   
-share/doc/phylip/consense.doc 
-share/doc/phylip/contchar.doc 
-share/doc/phylip/contml.doc   
-share/doc/phylip/contrast.doc 
-share/doc/phylip/discrete.doc 
-share/doc/phylip/distance.doc 
-share/doc/phylip/dnacomp.doc  
-share/doc/phylip/dnadist.doc  
-share/doc/phylip/dnainvar.doc 
-share/doc/phylip/dnaml.doc    
-share/doc/phylip/dnamlk.doc   
-share/doc/phylip/dnamove.doc  
-share/doc/phylip/dnapars.doc  
-share/doc/phylip/dnapenny.doc 
-share/doc/phylip/dollop.doc   
-share/doc/phylip/dolmove.doc  
-share/doc/phylip/dolpenny.doc 
-share/doc/phylip/draw.doc     
-share/doc/phylip/drawgram.doc 
-share/doc/phylip/drawtree.doc 
-share/doc/phylip/factor.doc   
-share/doc/phylip/fitch.doc    
-share/doc/phylip/gendist.doc  
-share/doc/phylip/kitsch.doc   
-share/doc/phylip/main.doc     
-share/doc/phylip/makeinf.doc  
-share/doc/phylip/mix.doc      
-share/doc/phylip/move.doc     
-share/doc/phylip/neighbor.doc 
-share/doc/phylip/penny.doc    
-share/doc/phylip/protdist.doc 
-share/doc/phylip/protml.doc   
-share/doc/phylip/protpars.doc 
-share/doc/phylip/restml.doc   
-share/doc/phylip/retree.doc   
-share/doc/phylip/seqboot.doc  
-share/doc/phylip/sequence.doc
+bin/treedist
+share/doc/phylip/clique.html
+share/doc/phylip/consense.html
+share/doc/phylip/contchar.html
+share/doc/phylip/contml.html
+share/doc/phylip/contrast.html
+share/doc/phylip/discrete.html
+share/doc/phylip/distance.html
+share/doc/phylip/dnacomp.html
+share/doc/phylip/dnadist.html
+share/doc/phylip/dnainvar.html
+share/doc/phylip/dnaml.html
+share/doc/phylip/dnamlk.html
+share/doc/phylip/dnamove.html
+share/doc/phylip/dnapars.html
+share/doc/phylip/dnapenny.html
+share/doc/phylip/dollop.html
+share/doc/phylip/dolmove.html
+share/doc/phylip/dolpenny.html
+share/doc/phylip/draw.html
+share/doc/phylip/drawgram.html
+share/doc/phylip/drawtree.html
+share/doc/phylip/factor.html
+share/doc/phylip/fitch.html
+share/doc/phylip/gendist.html
+share/doc/phylip/kitsch.html
+share/doc/phylip/main.html
+share/doc/phylip/mix.html
+share/doc/phylip/move.html
+share/doc/phylip/neighbor.html
+share/doc/phylip/pars.html
+share/doc/phylip/penny.html
+share/doc/phylip/phylip.gif
+share/doc/phylip/proml.html
+share/doc/phylip/protdist.html
+share/doc/phylip/protpars.html
+share/doc/phylip/restdist.html
+share/doc/phylip/restml.html
+share/doc/phylip/retree.html
+share/doc/phylip/seqboot.html
+share/doc/phylip/sequence.html
+share/doc/phylip/treedist.html
 @dirrm share/doc/phylip