Adding phylip version 3.5.

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.

PR:		19705
Submitted by:	David A. Bader <dbader@cielo.eece.unm.edu>

5 files changed, 161 insertions, 0 deletions

diff --git a/biology/phylip/Makefile b/biology/phylip/Makefile
new file mode 100644
index 00000000000..b7ec309be6f
--- /dev/null
+++ b/biology/phylip/Makefile
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+# New ports collection makefile for:	phylip
+# Date created:				4 July 2000
+# Whom:					dbader@eece.unm.edu
+#
+# $FreeBSD$
+#
+
+PORTNAME=	phylip
+PORTVERSION=	3.5
+CATEGORIES=	biology
+MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/phylip/
+DISTNAME=	${PORTNAME}
+EXTRACT_SUFX=	.tar.Z
+
+MAINTAINER=	dbader@eece.unm.edu
+
+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
+
+do-install:
+.for f in ${BINARIES}
+	${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
+.endfor
+.if !defined(NOPORTDOCS)
+	${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
+.for f in ${DOCFILES}
+	${INSTALL_DATA} ${WRKSRC}/${f} ${PREFIX}/share/doc/${PORTNAME}
+.endfor
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/phylip/distinfo b/biology/phylip/distinfo
new file mode 100644
index 00000000000..462e0c381b0
--- /dev/null
+++ b/biology/phylip/distinfo
@@ -0,0 +1 @@
+MD5 (phylip.tar.Z) = d437d19d82fd84c723a73b6420aae4fc
diff --git a/biology/phylip/pkg-comment b/biology/phylip/pkg-comment
new file mode 100644
index 00000000000..b6a5c95a716
--- /dev/null
+++ b/biology/phylip/pkg-comment
@@ -0,0 +1 @@
+A Phylogeny Inference Package
diff --git a/biology/phylip/pkg-descr b/biology/phylip/pkg-descr
new file mode 100644
index 00000000000..34988635d2f
--- /dev/null
+++ b/biology/phylip/pkg-descr
@@ -0,0 +1,45 @@
+              PHYLIP - Phylogeny Inference Package (version 3.5)
+
+     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
+
+There is also an Unsupported Division  containing  two  programs,  makeinf  and
+ProtML, which were contributed by others and are maintained by their authors.
+
+The package includes extensive documentation files that provide the information
+necessary to use and modify the programs.
+
+                             Joe Felsenstein
+                             joe@genetics.washington.edu
+                             Department of Genetics
+                             University of Washington
+                             Box 357360
+                             Seattle, Washington 98195-7360, U.S.A.
diff --git a/biology/phylip/pkg-plist b/biology/phylip/pkg-plist
new file mode 100644
index 00000000000..9c26e88aa18
--- /dev/null
+++ b/biology/phylip/pkg-plist
@@ -0,0 +1,70 @@
+bin/clique
+bin/consense
+bin/contml
+bin/contrast
+bin/dnacomp
+bin/dnadist
+bin/dnainvar
+bin/dnaml
+bin/dnamlk
+bin/dnamove
+bin/dnapars
+bin/dnapenny
+bin/dollop
+bin/dolmove
+bin/dolpenny
+bin/drawgram
+bin/drawtree
+bin/factor
+bin/fitch
+bin/gendist
+bin/kitsch
+bin/mix
+bin/move
+bin/neighbor
+bin/penny
+bin/protdist
+bin/protpars
+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
+@dirrm share/doc/phylip