diff --git a/biology/tRNAscan-SE/Makefile b/biology/tRNAscan-SE/Makefile
index 75658cb534c0..c80daf7fb373 100644
--- a/biology/tRNAscan-SE/Makefile
+++ b/biology/tRNAscan-SE/Makefile
@@ -1,24 +1,24 @@
 PORTNAME=	tRNAscan-SE
-PORTVERSION=	2.0.5
+PORTVERSION=	2.0.11
 CATEGORIES=	biology
 MASTER_SITES=	http://trna.ucsc.edu/software/
 DISTFILES=	${DISTNAME:tl}${EXTRACT_SUFX}
 
 MAINTAINER=	mzaki@e-mail.ne.jp
 COMMENT=	Searching for tRNA genes in genomic sequence
 WWW=		http://lowelab.ucsc.edu/tRNAscan-SE/
 
 LICENSE=	GPLv3+
 LICENSE_FILE=	${WRKSRC}/COPYING
 
 RUN_DEPENDS=	cmsearch:biology/infernal
 
-USES=		perl5 autoreconf
-
-WRKSRC=		${WRKDIR}/${DISTNAME:C,\.[0-9]+$,,}
+USES=		autoreconf perl5
 
 GNU_CONFIGURE=	yes
 
 MAKE_JOBS_UNSAFE=	yes
 
+WRKSRC=		${WRKDIR}/${DISTNAME:C,\.[0-9]+$,,}
+
 .include <bsd.port.mk>
diff --git a/biology/tRNAscan-SE/distinfo b/biology/tRNAscan-SE/distinfo
index a57336279094..8adefb253c6a 100644
--- a/biology/tRNAscan-SE/distinfo
+++ b/biology/tRNAscan-SE/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1578666520
-SHA256 (trnascan-se-2.0.5.tar.gz) = 92917c2dbec31f9cebef88671418696f077768f00fb7fe483be1a6093b4e7e60
-SIZE (trnascan-se-2.0.5.tar.gz) = 4373181
+TIMESTAMP = 1665480264
+SHA256 (trnascan-se-2.0.11.tar.gz) = 29b74edd0f84ad88139035e119b66397c54a37428e0b61c66a1b3d4733adcd1e
+SIZE (trnascan-se-2.0.11.tar.gz) = 4430973
diff --git a/biology/tRNAscan-SE/files/patch-Makefile.am b/biology/tRNAscan-SE/files/patch-Makefile.am
index 7a28de19c450..13be4377e71e 100644
--- a/biology/tRNAscan-SE/files/patch-Makefile.am
+++ b/biology/tRNAscan-SE/files/patch-Makefile.am
@@ -1,62 +1,62 @@
 --- Makefile.am.orig	2017-12-03 07:00:58 UTC
 +++ Makefile.am
 @@ -8,8 +8,8 @@
  AUTOMAKE_OPTIONS = foreign subdir-objects
  
  # set flags
 -AM_CFLAGS = -O
 -LDADD = -lm
 +#AM_CFLAGS = -O
 +#LDADD = -lm
  
  # macros for program dependencies
  EUFIND = src/eufind_const.h src/eufind_main.c src/pavesi.c
 @@ -23,20 +23,21 @@ COVESRC = src/align.c src/dbviterbi.c sr
  bin_PROGRAMS = bin/eufindtRNA bin/trnascan-1.4 bin/covels-SE bin/coves-SE
  bin_eufindtRNA_SOURCES = $(SQUIDHDRS) $(SQUIDSRC) $(EUFIND)
  bin_trnascan_1_4_SOURCES = src/trnascan.c
 -bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(libdir)\/tRNAscan-SE\/models\"  $(AM_CFLAGS)
 +bin_trnascan_1_4_CFLAGS = -DTSCANDIR=\"$(datadir)\/tRNAscan-SE\/models\"  $(AM_CFLAGS)
  bin_covels_SE_SOURCES = $(COVESRC) src/scan_main.c
  bin_coves_SE_SOURCES = $(COVESRC) src/score_main.c
  
  # process scripts
  # treat tRNAscan-SE.conf as a script since it's just easier
--dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf
-+dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE
+-dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE tRNAscan-SE.conf
++dist_bin_SCRIPTS = bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter bin/MitoHighConfidenceFilter tRNAscan-SE
 +sysconf_DATA = tRNAscan-SE.conf
  # for a few files, need to substitute perl path, bin directory, and lib directory
  # first, define a function for it
 -do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(libdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' 
 +do_subst = sed -e 's,\@bindir\@,$(bindir),g' -e 's,\@libdir\@,$(datadir),g' -e 's,\@sysconfdir\@,$(sysconfdir),g' -e 's,[@]PERL[@],$(PERL),g' -e 's,\@INFERNAL\@,$(INFERNAL),g' 
  
  # extra steps for cleaning/distribution
  CLEANFILES = $(dist_bin_SCRIPTS) $(srcdir)/lib/*
 -include_HEADERS = $(srcdir)/src/*.h 
 +#include_HEADERS = $(srcdir)/src/*.h 
- EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter tRNAscan-SE.src tRNAscan-SE.conf.src 
+ EXTRA_DIST = lib src/sstofa.in src/fasta2gsi.in EukHighConfidenceFilter MitoHighConfidenceFilter tRNAscan-SE.src tRNAscan-SE.conf.src 
  
  # then create build rules
 @@ -61,16 +62,9 @@ bin/EukHighConfidenceFilter: EukHighConf
  	$(do_subst) < $(srcdir)/EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter
  	chmod +x bin/EukHighConfidenceFilter
  
 -# copy libraries. We don't have "libraries" in the libgmp.so.4 kind, but we do have data libraries, so we don't have to deal with lib_LTLIBRARIES.
 -install-data-hook:
 -	chmod u+w $(exec_prefix)
 -	test -d $(libdir) || mkdir $(libdir)
 -	chmod u+w $(libdir)
 -	test -d $(libdir)/tRNAscan-SE || mkdir $(libdir)/tRNAscan-SE
 -	cp -rf $(srcdir)/lib/* $(libdir)/tRNAscan-SE 
 -
 -# remove lib/ files during uninstallation. A bit of a hack, since lib files are write-protected by default. Files 
 -uninstall-hook:
 -	chmod -R u+w $(libdir)/tRNAscan-SE
 -	rm -rf $(libdir)/tRNAscan-SE
 -
 +gcodedir = $(pkgdatadir)/gcode
 +modelsdir = $(pkgdatadir)/models
 +modulesdir = $(pkgdatadir)/tRNAscanSE
 +dist_gcode_DATA = lib/gcode/*
 +dist_models_DATA = lib/models/*
 +dist_modules_DATA = lib/tRNAscanSE/*
diff --git a/biology/tRNAscan-SE/pkg-plist b/biology/tRNAscan-SE/pkg-plist
index bb3ebb6f07a9..6dbe93e6916f 100644
--- a/biology/tRNAscan-SE/pkg-plist
+++ b/biology/tRNAscan-SE/pkg-plist
@@ -1,136 +1,140 @@
 bin/EukHighConfidenceFilter
+bin/MitoHighConfidenceFilter
 bin/covels-SE
 bin/coves-SE
 bin/eufindtRNA
 bin/fasta2gsi
 bin/sstofa
 bin/tRNAscan-SE
 bin/trnascan-1.4
 etc/tRNAscan-SE.conf
 %%DATADIR%%/gcode/gcode.cilnuc
 %%DATADIR%%/gcode/gcode.echdmito
 %%DATADIR%%/gcode/gcode.invmito
+%%DATADIR%%/gcode/gcode.marsumito
 %%DATADIR%%/gcode/gcode.othmito
 %%DATADIR%%/gcode/gcode.vertmito
 %%DATADIR%%/gcode/gcode.ystmito
 %%DATADIR%%/models/Cren-eury-BHB-noncan.cm
 %%DATADIR%%/models/Dsignal
 %%DATADIR%%/models/ESELC.cm
 %%DATADIR%%/models/PSELC.cm
 %%DATADIR%%/models/TPCsignal
 %%DATADIR%%/models/TRNA2-arch.cm
 %%DATADIR%%/models/TRNA2-archns.cm
 %%DATADIR%%/models/TRNA2-bact.cm
 %%DATADIR%%/models/TRNA2-bactns.cm
 %%DATADIR%%/models/TRNA2-euk.cm
 %%DATADIR%%/models/TRNA2-eukns.cm
 %%DATADIR%%/models/TRNA2.cm
 %%DATADIR%%/models/TRNA2ns.cm
 %%DATADIR%%/models/TRNAinf-1415-ns.cm
 %%DATADIR%%/models/TRNAinf-1415.cm
 %%DATADIR%%/models/TRNAinf-arch-3h.cm
 %%DATADIR%%/models/TRNAinf-arch-5h.cm
 %%DATADIR%%/models/TRNAinf-arch-SeC.cm
 %%DATADIR%%/models/TRNAinf-arch-iso
 %%DATADIR%%/models/TRNAinf-arch-iso.i1f
 %%DATADIR%%/models/TRNAinf-arch-iso.i1i
 %%DATADIR%%/models/TRNAinf-arch-iso.i1m
 %%DATADIR%%/models/TRNAinf-arch-iso.i1p
 %%DATADIR%%/models/TRNAinf-arch-ns.cm
 %%DATADIR%%/models/TRNAinf-arch.cm
 %%DATADIR%%/models/TRNAinf-bact-SeC.cm
 %%DATADIR%%/models/TRNAinf-bact-iso
 %%DATADIR%%/models/TRNAinf-bact-iso.i1f
 %%DATADIR%%/models/TRNAinf-bact-iso.i1i
 %%DATADIR%%/models/TRNAinf-bact-iso.i1m
 %%DATADIR%%/models/TRNAinf-bact-iso.i1p
 %%DATADIR%%/models/TRNAinf-bact-ns.cm
 %%DATADIR%%/models/TRNAinf-bact.cm
 %%DATADIR%%/models/TRNAinf-euk-SeC.cm
 %%DATADIR%%/models/TRNAinf-euk-iso
 %%DATADIR%%/models/TRNAinf-euk-iso.i1f
 %%DATADIR%%/models/TRNAinf-euk-iso.i1i
 %%DATADIR%%/models/TRNAinf-euk-iso.i1m
 %%DATADIR%%/models/TRNAinf-euk-iso.i1p
 %%DATADIR%%/models/TRNAinf-euk-ns.cm
 %%DATADIR%%/models/TRNAinf-euk.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal
 %%DATADIR%%/models/TRNAinf-mito-mammal-Ala.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Arg.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Asn.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Asp.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Cys.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Gln.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Glu.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Gly.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-His.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Ile.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-LeuTAA.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-LeuTAG.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Lys.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Met.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Phe.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Pro.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-SerGCT.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-SerTGA.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Thr.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Trp.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Tyr.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal-Val.cm
 %%DATADIR%%/models/TRNAinf-mito-mammal.i1f
 %%DATADIR%%/models/TRNAinf-mito-mammal.i1i
 %%DATADIR%%/models/TRNAinf-mito-mammal.i1m
 %%DATADIR%%/models/TRNAinf-mito-mammal.i1p
 %%DATADIR%%/models/TRNAinf-mito-vert
 %%DATADIR%%/models/TRNAinf-mito-vert-Ala.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Arg.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Asn.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Asp.cm
+%%DATADIR%%/models/TRNAinf-mito-vert-Cys-no-darm.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Cys.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Gln.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Glu.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Gly.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-His.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Ile.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-LeuTAA.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-LeuTAG.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Lys.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Met.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Phe.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Pro.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-SerGCT.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-SerTGA.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Thr.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Trp.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Tyr.cm
 %%DATADIR%%/models/TRNAinf-mito-vert-Val.cm
 %%DATADIR%%/models/TRNAinf-mito-vert.i1f
 %%DATADIR%%/models/TRNAinf-mito-vert.i1i
 %%DATADIR%%/models/TRNAinf-mito-vert.i1m
 %%DATADIR%%/models/TRNAinf-mito-vert.i1p
 %%DATADIR%%/models/TRNAinf-ns.cm
 %%DATADIR%%/models/TRNAinf.cm
 %%DATADIR%%/models/Thaum-BHB-noncan.cm
 %%DATADIR%%/tRNAscanSE/ArrayCMscanResults.pm
 %%DATADIR%%/tRNAscanSE/ArraytRNA.pm
 %%DATADIR%%/tRNAscanSE/CM.pm
 %%DATADIR%%/tRNAscanSE/CMscanResultFile.pm
 %%DATADIR%%/tRNAscanSE/Configuration.pm
+%%DATADIR%%/tRNAscanSE/Constants.pm
 %%DATADIR%%/tRNAscanSE/Eufind.pm
 %%DATADIR%%/tRNAscanSE/FpScanResultFile.pm
 %%DATADIR%%/tRNAscanSE/GeneticCode.pm
 %%DATADIR%%/tRNAscanSE/IntResultFile.pm
 %%DATADIR%%/tRNAscanSE/LogFile.pm
 %%DATADIR%%/tRNAscanSE/MultiResultFile.pm
 %%DATADIR%%/tRNAscanSE/Options.pm
 %%DATADIR%%/tRNAscanSE/ResultFileReader.pm
 %%DATADIR%%/tRNAscanSE/SS.pm
 %%DATADIR%%/tRNAscanSE/ScanResult.pm
 %%DATADIR%%/tRNAscanSE/Sequence.pm
 %%DATADIR%%/tRNAscanSE/SprinzlAlign.pm
 %%DATADIR%%/tRNAscanSE/SprinzlAlignResults.pm
 %%DATADIR%%/tRNAscanSE/SprinzlPos.pm
 %%DATADIR%%/tRNAscanSE/Stats.pm
 %%DATADIR%%/tRNAscanSE/Tscan.pm
 %%DATADIR%%/tRNAscanSE/Utils.pm
 %%DATADIR%%/tRNAscanSE/tRNA.pm