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authorrh <rh>1999-07-28 20:18:55 +0000
committerrh <rh>1999-07-28 20:18:55 +0000
commitb14b0f36d034f3a652b6c77a1879f09a06bac843 (patch)
tree7436140052c23be950e0418f675d071a895150bc /biology/fastDNAml
parentcdf06712ea0c37b3fd54b8b620d05ad0be4d26fc (diff)
downloadpkgsrc-b14b0f36d034f3a652b6c77a1879f09a06bac843.tar.gz
Import of fastDNAml-1.2.1, a program for estimating maximum likelihood
phylogenetic trees from nucleotide sequences, as submitted by Marc Baudoin, thanks!
Diffstat (limited to 'biology/fastDNAml')
-rw-r--r--biology/fastDNAml/Makefile33
-rw-r--r--biology/fastDNAml/files/md53
-rw-r--r--biology/fastDNAml/pkg/COMMENT1
-rw-r--r--biology/fastDNAml/pkg/DESCR8
-rw-r--r--biology/fastDNAml/pkg/PLIST38
5 files changed, 83 insertions, 0 deletions
diff --git a/biology/fastDNAml/Makefile b/biology/fastDNAml/Makefile
new file mode 100644
index 00000000000..a631053f116
--- /dev/null
+++ b/biology/fastDNAml/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD: Makefile,v 1.1.1.1 1999/07/28 20:18:55 rh Exp $
+
+DISTNAME= fastDNAml_1.2.1
+PKGNAME= fastDNAml-1.2.1
+WRKSRC= ${WRKDIR}/${DISTNAME}
+CATEGORIES= biology
+MASTER_SITES= http://geta.life.uiuc.edu/~gary/programs/fastDNAml/
+
+MAINTAINER= babafou@babafou.eu.org
+HOMEPAGE= http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
+
+NO_CDROM= "No commercial distribution without a royalty agreement with the author"
+
+do-build :
+ @ cd ${WRKSRC}/source && ${MAKE} LDFLAGS=-lm fastDNAml
+
+do-install :
+ ${INSTALL_PROGRAM} ${WRKSRC}/source/fastDNAml ${PREFIX}/bin
+.for SCRIPT in ae2dnaml bootstrap categories categories_file \
+ checkpoint_summary clean_checkpoints clean_jumbles \
+ dnaml_progress fastDNAml_boot fastDNAml_loop \
+ frequencies global iterate_rates jumble min_info \
+ n_categories n_files out.PID outgroup printdata \
+ quickadd restart scores transition treefile \
+ treefile2prolog trees2NEXUS trees2prolog userlengths \
+ usertree usertrees weights weights_categories
+ ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${SCRIPT} ${PREFIX}/bin
+.endfor
+ ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/fastDNAml
+ ${INSTALL_DATA} ${WRKSRC}/docs/fastDNAml_doc_1.2.txt ${PREFIX}/share/doc/fastDNAml
+ ${INSTALL_DATA} ${WRKSRC}/docs/fastDNAml_scripts.txt ${PREFIX}/share/doc/fastDNAml
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/fastDNAml/files/md5 b/biology/fastDNAml/files/md5
new file mode 100644
index 00000000000..5128b78c851
--- /dev/null
+++ b/biology/fastDNAml/files/md5
@@ -0,0 +1,3 @@
+$NetBSD: md5,v 1.1.1.1 1999/07/28 20:18:55 rh Exp $
+
+MD5 (fastDNAml_1.2.1.tar.gz) = 61bb05165810ff6813ee13624ab08511
diff --git a/biology/fastDNAml/pkg/COMMENT b/biology/fastDNAml/pkg/COMMENT
new file mode 100644
index 00000000000..a6186cff654
--- /dev/null
+++ b/biology/fastDNAml/pkg/COMMENT
@@ -0,0 +1 @@
+Program derived from Joseph Felsenstein's version 3.3 DNAML
diff --git a/biology/fastDNAml/pkg/DESCR b/biology/fastDNAml/pkg/DESCR
new file mode 100644
index 00000000000..9a8cffffa5a
--- /dev/null
+++ b/biology/fastDNAml/pkg/DESCR
@@ -0,0 +1,8 @@
+fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
+(part of his PHYLIP package). Users should consult the documentation for
+DNAML before using this program.
+
+fastDNAml is an attempt to solve the same problem as DNAML, but to do so
+faster and using less memory, so that larger trees and/or more bootstrap
+replicates become tractable. Much of fastDNAml is merely a recoding of the
+PHYLIP 3.3 DNAML program from PASCAL to C.
diff --git a/biology/fastDNAml/pkg/PLIST b/biology/fastDNAml/pkg/PLIST
new file mode 100644
index 00000000000..dd90ff93ad5
--- /dev/null
+++ b/biology/fastDNAml/pkg/PLIST
@@ -0,0 +1,38 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 1999/07/28 20:18:56 rh Exp $
+bin/fastDNAml
+bin/ae2dnaml
+bin/bootstrap
+bin/categories
+bin/categories_file
+bin/checkpoint_summary
+bin/clean_checkpoints
+bin/clean_jumbles
+bin/dnaml_progress
+bin/fastDNAml_boot
+bin/fastDNAml_loop
+bin/frequencies
+bin/global
+bin/iterate_rates
+bin/jumble
+bin/min_info
+bin/n_categories
+bin/n_files
+bin/out.PID
+bin/outgroup
+bin/printdata
+bin/quickadd
+bin/restart
+bin/scores
+bin/transition
+bin/treefile
+bin/treefile2prolog
+bin/trees2NEXUS
+bin/trees2prolog
+bin/userlengths
+bin/usertree
+bin/usertrees
+bin/weights
+bin/weights_categories
+share/doc/fastDNAml/fastDNAml_doc_1.2.txt
+share/doc/fastDNAml/fastDNAml_scripts.txt
+@dirrm share/doc/fastDNAml