Index: Makefile
===================================================================
--- Makefile	(revision 453805)
+++ Makefile	(working copy)
@@ -2,32 +2,32 @@
 # $FreeBSD$
 
 PORTNAME=	hmmer
-PORTVERSION=	3.0
-PORTREVISION=	1
+PORTVERSION=	3.1b2
 CATEGORIES=	biology
-MASTER_SITES=	ftp://selab.janelia.org/pub/software/hmmer3/3.0/ \
-		http://selab.janelia.org/software/hmmer3/3.0/
+MASTER_SITES=	http://eddylab.org/software/hmmer3/${PORTVERSION}/
 
 MAINTAINER=	bacon4000@gmail.com
 COMMENT=	Profile hidden Markov models for biological sequence analysis
 
-BROKEN=		No public distfiles
-
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+USES=		gmake
 GNU_CONFIGURE=	yes
-USES=		perl5
-CONFIGURE_ARGS+=--enable-threads
+MAKE_ARGS=	V=1
 
-DOCFILES=	COPYRIGHT INSTALL LICENSE Userguide.pdf
-EXAMPLES=	7LESS_DROME Pkinase.sto fn3.sto globins4.sto minifam.h3f minifam.h3p \
-		HBB_HUMAN fn3.hmm globins4.hmm globins45.fa minifam.h3i \
-		Pkinase.hmm fn3.out globins4.out minifam minifam.h3m
+OPTIONS_DEFINE=	DOCS EXAMPLES TEST
+TEST_TEST_TARGET=	check
+TEST_USES=	shebangfix perl5
+TEST_VARS=	shebang_glob=*.pl shebang_files=easel/devkit/*
 
-OPTIONS_DEFINE=	DOCS EXAMPLES
+DOCFILES=	COPYRIGHT Userguide.pdf
+EXAMPLES=	7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.out MADE1.sto \
+		Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.out fn3.sto \
+		globins4.hmm globins4.out globins4.sto globins45.fa \
+		minifam minifam.h3f minifam.h3i minifam.h3m minifam.h3p
 
-.include <bsd.port.options.mk>
+.include <bsd.port.pre.mk>
 
 # HMMER is useless without SSE and any PC in use today should support it
 # Should probably also do enable-vmx on Power processors to enable
@@ -36,14 +36,17 @@
 CONFIGURE_ARGS+=--enable-sse
 .endif
 
+post-build-TEST-on:	do-test
+
 post-install:
 	@${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*
-	(cd ${WRKSRC}/documentation/man; for i in *.man; do \
-		${INSTALL_MAN} $$i ${STAGEDIR}${PREFIX}/man/man1/`echo $$i|${SED} 's/.man/.1/'`; \
-	done)
+
+post-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR}
+
+post-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR}
 
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
Index: distinfo
===================================================================
--- distinfo	(revision 453805)
+++ distinfo	(working copy)
@@ -1,2 +1,3 @@
-SHA256 (hmmer-3.0.tar.gz) = 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83
-SIZE (hmmer-3.0.tar.gz) = 3952015
+TIMESTAMP = 1510218548
+SHA256 (hmmer-3.1b2.tar.gz) = dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536
+SIZE (hmmer-3.1b2.tar.gz) = 5965253
Index: pkg-descr
===================================================================
--- pkg-descr	(revision 453805)
+++ pkg-descr	(working copy)
@@ -7,4 +7,4 @@
 a sequence database to find (and/or align) additional homologues of the
 sequence family.
 
-WWW: http://hmmer.janelia.org/
+WWW: http://hmmer.org/
Index: pkg-plist
===================================================================
--- pkg-plist	(revision 453805)
+++ pkg-plist	(working copy)
@@ -1,8 +1,13 @@
+bin/alimask
 bin/hmmalign
 bin/hmmbuild
+bin/hmmc2
 bin/hmmconvert
 bin/hmmemit
+bin/hmmerfm-exactmatch
 bin/hmmfetch
+bin/hmmlogo
+bin/hmmpgmd
 bin/hmmpress
 bin/hmmscan
 bin/hmmsearch
@@ -9,7 +14,20 @@
 bin/hmmsim
 bin/hmmstat
 bin/jackhmmer
+bin/makehmmerdb
+bin/nhmmer
+bin/nhmmscan
 bin/phmmer
+include/cachedb.h
+include/hmmer.h
+include/impl_sse.h
+include/p7_config.h
+include/p7_gbands.h
+include/p7_gmxb.h
+include/p7_gmxchk.h
+include/p7_hmmcache.h
+lib/libhmmer.a
+man/man1/alimask.1.gz
 man/man1/hmmalign.1.gz
 man/man1/hmmbuild.1.gz
 man/man1/hmmconvert.1.gz
@@ -16,6 +34,8 @@
 man/man1/hmmemit.1.gz
 man/man1/hmmer.1.gz
 man/man1/hmmfetch.1.gz
+man/man1/hmmlogo.1.gz
+man/man1/hmmpgmd.1.gz
 man/man1/hmmpress.1.gz
 man/man1/hmmscan.1.gz
 man/man1/hmmsearch.1.gz
@@ -22,24 +42,29 @@
 man/man1/hmmsim.1.gz
 man/man1/hmmstat.1.gz
 man/man1/jackhmmer.1.gz
+man/man1/makehmmerdb.1.gz
+man/man1/nhmmer.1.gz
+man/man1/nhmmscan.1.gz
 man/man1/phmmer.1.gz
 %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
-%%PORTDOCS%%%%DOCSDIR%%/INSTALL
-%%PORTDOCS%%%%DOCSDIR%%/LICENSE
 %%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.out
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p