[svn-upgrade] Integrating new upstream version, ncbi-tools6 (6.1.20070822)

19 files changed, 1281 insertions, 67 deletions

diff --git a/data/16Score.nhr b/data/16SCore.nhr
index 734bc148..734bc148 100755..100644
--- a/data/16Score.nhr
+++ b/data/16SCore.nhr
diff --git a/data/16Score.nin b/data/16SCore.nin
index 3eef5310..3eef5310 100755..100644
--- a/data/16Score.nin
+++ b/data/16SCore.nin
diff --git a/data/16Score.nsq b/data/16SCore.nsq
index d3b3a3db..d3b3a3db 100755..100644
--- a/data/16Score.nsq
+++ b/data/16SCore.nsq
diff --git a/data/Combined16SrRNA.nhr b/data/Combined16SrRNA.nhr
new file mode 100644
index 00000000..1679ccb4
--- /dev/null
+++ b/data/Combined16SrRNA.nhr
diff --git a/data/Combined16SrRNA.nin b/data/Combined16SrRNA.nin
new file mode 100644
index 00000000..a1f8b98d
--- /dev/null
+++ b/data/Combined16SrRNA.nin
diff --git a/data/Combined16SrRNA.nsq b/data/Combined16SrRNA.nsq
new file mode 100644
index 00000000..d3348a14
--- /dev/null
+++ b/data/Combined16SrRNA.nsq
diff --git a/data/UniVec.nhr b/data/UniVec.nhr
index a4b82646..bf9e200e 100644
--- a/data/UniVec.nhr
+++ b/data/UniVec.nhr
diff --git a/data/UniVec.nin b/data/UniVec.nin
index ab269bd2..e48d39a7 100644
--- a/data/UniVec.nin
+++ b/data/UniVec.nin
diff --git a/data/UniVec.nsq b/data/UniVec.nsq
index ebc1f6df..7b4b2848 100644
--- a/data/UniVec.nsq
+++ b/data/UniVec.nsq
diff --git a/data/UniVec_Core.nhr b/data/UniVec_Core.nhr
index db0a8953..fb45ddeb 100644
--- a/data/UniVec_Core.nhr
+++ b/data/UniVec_Core.nhr
diff --git a/data/UniVec_Core.nin b/data/UniVec_Core.nin
index 4ed53c63..4fc64215 100644
--- a/data/UniVec_Core.nin
+++ b/data/UniVec_Core.nin
diff --git a/data/UniVec_Core.nsq b/data/UniVec_Core.nsq
index 71cf3188..b7943782 100644
--- a/data/UniVec_Core.nsq
+++ b/data/UniVec_Core.nsq
diff --git a/data/country_lat_lon.txt b/data/country_lat_lon.txt
new file mode 100644
index 00000000..2814ddc6
--- /dev/null
+++ b/data/country_lat_lon.txt
@@ -0,0 +1,346 @@
+Afghanistan	AF	60.4	29.3	74.9	38.5
+Albania	AL	19.2	39.6	21.1	42.7
+Algeria	AG	-8.7	18.9	12.0	37.1
+American Samoa	AQ	-171.1	-11.1	-171.1	-11.0	-170.9	-14.4	-169.4	-14.2
+Andorra	AN	1.4	42.4	1.8	42.7
+Angola	AO	11.6	-18.1	24.1	-4.4
+Anguilla	AV	-63.2	18.1	-62.9	18.3
+Antarctica	AY	
+Antigua and Barbuda	AC	-62.4	16.9	-62.3	16.9	-62.0	16.9	-61.7	17.7
+Arctic Ocean	XX	
+Argentina	AR	-73.6	-55.1	-53.6	-21.8
+Armenia	AM	43.4	38.8	46.6	41.3
+Aruba	AA	-70.1	12.4	-69.8	12.7
+Ashmore and Cartier Islands	AT	122.9	-12.3	123.1	-12.1
+Atlantic Ocean	XX	
+Australia	AS	112.9	-43.7	153.6	-10.0
+Australia: Australian Capital Territory	XX	148.7	-36.0	149.4	-35.1
+Australia: Jervis Bay Territory	XX	150.5	-35.2	150.8	-35.1
+Australia: New South Wales	XX	140.9	-37.6	153.6	-28.2
+Australia: Northern Territory	XX	128.9	-26.1	138.0	-10.9
+Australia: Queensland	XX	137.9	-29.2	153.6	-10.0
+Australia: South Australia	XX	128.9	-38.1	141.0	-26.0
+Australia: Tasmania	XX	143.8	-43.7	148.5	-39.6
+Australia: Victoria	XX	140.9	-39.6	150.0	-34.0
+Australia: Western Australia	XX	112.9	-35.2	129.0	-13.7
+Austria	AU	9.5	46.3	17.2	49.0
+Azerbaijan	AJ	45.0	38.3	50.6	41.9
+Bahamas	BF	-79.7	20.9	-72.7	27.2
+Bahrain	BA	50.3	25.7	50.7	26.3
+Baker Island	FQ	-176.5	0.1	-176.5	0.2
+Bangladesh	BG	88.0	20.5	92.7	26.6
+Barbados	BB	-59.7	13.0	-59.4	13.3
+Bassas da India	BS	39.6	-21.6	39.8	-21.4
+Belarus	BO	23.1	51.2	32.8	56.2
+Belgium	BE	2.5	49.4	6.4	51.5
+Belize	BH	-89.3	15.8	-86.9	18.5
+Benin	BN	0.7	6.2	3.9	12.4
+Bermuda	BD	-64.9	32.2	-64.7	32.4
+Bhutan	BT	88.7	26.7	92.1	28.3
+Bolivia	BL	-69.7	-22.9	-57.5	-9.7
+Bosnia and Herzegovina	BK	15.7	42.5	19.7	45.3
+Botswana	BC	19.9	-27.0	29.4	-17.8
+Bouvet Island	BV	3.3	-54.5	3.5	-54.4
+Brazil	BR	-74.0	-33.8	-34.8	5.0
+British Virgin Islands	VI	-64.8	18.2	-63.2	18.8
+Brunei	BX	114.0	4.0	115.4	5.0
+Bulgaria	BU	22.3	41.2	28.6	44.2
+Burkina Faso	UV	-5.6	9.4	2.4	15.1
+Burundi	BY	28.9	-4.5	30.8	-2.3
+Cambodia	CB	102.3	9.2	107.6	14.7
+Cameroon	CM	8.4	1.6	16.2	13.1
+Canada	CA	-141.0	41.7	-52.6	83.1
+Canada: Alberta	XX	-120.0	48.9	-110.0	60.0
+Canada: British Columbia	XX	-139.1	48.3	-114.1	60.0
+Canada: Manitoba	XX	-102.1	48.9	-89.0	60.0
+Canada: New Brunswick	XX	-69.1	44.5	-63.8	48.1
+Canada: Newfoundland and Labrador	XX	-67.9	46.6	-52.6	60.4
+Canada: Northwest Territories	XX	-136.5	60.0	-102.0	78.8
+Canada: Nova Scotia	XX	-66.4	43.3	-59.7	47.0
+Canada: Nunavut	XX	-120.4	60.0	-61.2	83.1
+Canada: Ontario	XX	-95.2	41.6	-74.3	56.9
+Canada: Prince Edward Island	XX	-64.5	45.9	-62.0	47.1
+Canada: Quebec	XX	-79.8	45.0	-57.1	62.6
+Canada: Saskatchewan	XX	-110.0	48.9	-101.4	60.0
+Canada: Yukon	XX	-141.0	60.0	-124.0	69.6
+Cape Verde	CV	-25.4	14.8	-22.7	17.2
+Cayman Islands	CJ	-81.5	19.2	-81.1	19.4	-80.2	19.6	-79.7	19.8
+Central African Republic	CT	14.4	2.2	27.5	11.0
+Chad	CD	13.4	7.4	24.0	23.5
+Chile	CI	-75.8	-56.0	-66.4	-17.5
+China	CH	73.5	20.2	134.8	53.6
+Christmas Island	KT	105.5	-10.6	105.7	-10.4
+Clipperton Island	IP	-109.3	10.2	-109.2	10.3
+Cocos Islands	CK	96.8	-12.2	96.9	-11.8
+Colombia	CO	-79.1	-4.3	-66.9	12.5
+Comoros	CN	43.2	-12.5	44.5	-11.4
+Cook Islands	CW	-159.9	-22.0	-157.3	-18.8
+Coral Sea Islands	CR	
+Costa Rica	CS	-87.1	5.4	-87.0	5.6	-86.0	8.0	-82.6	11.2
+Cote d'Ivoire	IV	-8.6	4.3	-2.5	10.7
+Croatia	HR	13.4	42.3	19.4	46.5
+Cuba	CU	-85.0	19.8	-74.1	23.3
+Cyprus	CY	32.2	34.5	34.6	35.7
+Czech Republic	EZ	12.0	48.5	18.9	51.0
+Democratic Republic of the Congo	CG	12.2	-13.5	31.3	5.4
+Denmark	DA	8.0	54.5	12.7	57.7	14.6	54.9	15.2	55.3
+Djibouti	DJ	41.7	10.9	43.4	12.7
+Dominica	DO	-61.5	15.2	-61.2	15.6
+Dominican Republic	DR	-72.1	17.4	-68.3	19.9
+East Timor	TT	124.9	-9.5	127.4	-8.3
+Ecuador	EC	-92.1	-1.5	-89.2	1.7	-81.1	-5.0	-75.2	1.4
+Ecuador: Galapagos	XX	-92.1	-1.5	-89.2	1.7
+Egypt	EG	24.6	21.7	35.8	31.7
+El Salvador	ES	-90.2	13.1	-87.7	14.4
+Equatorial Guinea	EK	8.4	3.2	8.9	3.8	9.2	0.8	11.3	2.3
+Eritrea	ER	36.4	12.3	43.1	18.0
+Estonia	EN	21.7	57.5	28.2	59.7
+Ethiopia	ET	32.9	3.4	48.0	14.9
+Europa Island	EU	40.3	-22.4	40.4	-22.3
+Falkland Islands (Islas Malvinas)	FK	-61.4	-53.0	-57.7	-51.0
+Faroe Islands	FO	-7.7	61.3	-6.3	62.4
+Fiji	FJ	-180.0	-20.7	-178.2	-15.7	-175.7	-19.8	-175.0	-15.6	176.8	-19.3	180.0	-12.5
+Finland	FI	19.3	59.7	31.6	70.1
+France	FR	-5.2	42.3	8.2	51.1	8.5	41.3	9.6	43.0
+France: Corsica	XX	8.5	41.3	9.6	43.0
+French Guiana	FG	-54.6	2.1	-51.6	5.8
+French Polynesia	FP	-154.7	-27.7	-134.9	-7.8
+French Southern and Antarctic Lands	FS	68.6	-49.8	70.6	-48.5
+Gabon	GB	8.6	-4.0	14.5	2.3
+Gambia	GA	-16.9	13.0	-13.8	13.8
+Gaza Strip	GZ	34.2	31.2	34.5	31.6
+Georgia	GG	40.0	41.0	46.7	43.6
+Germany	GM	5.8	47.2	15.0	55.1
+Ghana	GH	-3.3	4.7	1.2	11.2
+Gibraltar	GI	-5.4	36.1	-5.3	36.2
+Glorioso Islands	GO	47.2	-11.6	47.4	-11.5
+Greece	GR	19.3	34.8	28.2	41.8
+Greenland	GL	-73.3	59.7	-11.3	83.6
+Grenada	GJ	-61.8	11.9	-61.6	12.3
+Guadeloupe	GP	-63.2	17.8	-62.8	18.1	-61.9	15.8	-61.0	16.5
+Guam	GQ	144.6	13.2	145.0	13.7
+Guatemala	GT	-92.3	13.7	-88.2	17.8
+Guernsey	GK	-2.7	49.4	-2.4	49.5
+Guinea	GV	-15.1	7.1	-7.6	12.7
+Guinea-Bissau	PU	-16.8	10.8	-13.6	12.7
+Guyana	GY	-61.4	1.1	-56.5	8.6
+Haiti	HA	-74.5	18.0	-71.6	20.1
+Heard Island and McDonald Islands	HM	73.2	-53.2	73.7	-52.9
+Honduras	HO	-89.4	12.9	-83.2	16.5
+Hong Kong	HK	113.8	22.1	114.4	22.6
+Howland Island	HQ	-176.7	0.7	-176.6	0.8
+Hungary	HU	16.1	45.7	22.9	48.6
+Iceland	IC	-24.6	63.2	-13.5	66.6
+India	IN	67.3	8.0	97.4	35.5
+Indian Ocean	XX	
+Indonesia	ID	95.0	-11.1	141.0	5.9
+Iran	IR	44.0	25.0	63.3	39.8
+Iraq	IZ	38.8	29.1	48.6	37.4
+Ireland	EI	-10.7	51.4	-6.0	55.4
+Isle of Man	IM	-4.9	54.0	-4.3	54.4
+Israel	IS	34.2	29.4	35.7	33.3
+Italy	IT	6.6	35.4	18.5	47.1
+Jamaica	JM	-78.4	17.7	-76.2	18.5
+Jan Mayen	JN	-9.1	70.8	-7.9	71.2
+Japan	JA	122.9	24.0	125.5	25.9	126.7	20.5	145.8	45.5
+Jarvis Island	DQ	-160.1	-0.4	-160.0	-0.4
+Jersey	JE	-2.3	49.1	-2.0	49.3
+Johnston Atoll	JQ	-169.6	16.7	-169.4	16.8
+Jordan	JO	34.9	29.1	39.3	33.4
+Juan de Nova Island	JU	42.6	-17.1	42.8	-16.8
+Kazakhstan	KZ	46.4	40.9	87.3	55.4
+Kenya	KE	33.9	-4.7	41.9	4.6
+Kerguelen Archipelago	XX	
+Kingman Reef	KQ	-162.9	6.1	-162.4	6.7
+Kiribati	KR	172.6	0.1	173.9	3.4	174.2	-2.7	176.9	-0.5
+Kuwait	KU	46.5	28.5	48.4	30.1
+Kyrgyzstan	KG	69.2	39.1	80.3	43.2
+Laos	LA	100.0	13.9	107.7	22.5
+Latvia	LG	20.9	55.6	28.2	58.1
+Lebanon	LE	35.1	33.0	36.6	34.7
+Lesotho	LT	27.0	-30.7	29.5	-28.6
+Liberia	LI	-11.5	4.3	-7.4	8.6
+Libya	LY	9.3	19.5	25.2	33.2
+Liechtenstein	LS	9.4	47.0	9.6	47.3
+Lithuania	LH	20.9	53.9	26.9	56.4
+Luxembourg	LU	5.7	49.4	6.5	50.2
+Macau	MC	113.5	22.1	113.6	22.2
+Macedonia	MK	20.4	40.8	23.0	42.4
+Madagascar	MA	43.1	-25.7	50.5	-11.9
+Malawi	MI	32.6	-17.2	35.9	-9.4
+Malaysia	MY	98.9	5.6	98.9	5.7	99.6	1.2	104.5	6.7	109.5	0.8	119.3	7.4
+Maldives	MV	72.6	-0.7	73.7	7.1
+Mali	ML	-12.3	10.1	4.2	25.0
+Malta	MT	14.1	35.8	14.6	36.1
+Marshall Islands	RM	160.7	4.5	172.0	14.8
+Martinique	MB	-61.3	14.3	-60.8	14.9
+Mauritania	MR	-17.1	14.7	-4.8	27.3
+Mauritius	MP	57.3	-20.6	57.8	-20.0	59.5	-16.9	59.6	-16.7
+Mayotte	MF	45.0	-13.1	45.3	-12.6
+Mexico	MX	-118.5	28.8	-118.3	29.2	-117.3	14.5	-86.7	32.7
+Micronesia	FM	138.0	9.4	138.2	9.6	139.6	9.8	139.8	10.0	140.5	9.7	140.5	9.8	147.0	7.3	147.0	7.4	149.3	6.6	149.3	6.7	151.5	7.1	152.0	7.5	153.5	5.2	153.8	5.6	157.1	5.7	160.7	7.1	162.9	5.2	163.0	5.4
+Midway Islands	MQ	-178.4	28.3	-178.3	28.4	-177.4	28.1	-177.3	28.2	-174.0	26.0	-174.0	26.1	-171.8	25.7	-171.7	25.8
+Moldova	MD	26.6	45.4	30.2	48.5
+Monaco	MN	7.3	43.7	7.5	43.8
+Mongolia	MG	87.7	41.5	119.9	52.2
+Montenegro	MJ	18.4	42.2	20.4	43.6
+Montserrat	MH	-62.3	16.6	-62.1	16.8
+Morocco	MO	-13.2	27.6	-1.0	35.9
+Mozambique	MZ	30.2	-26.9	40.8	-10.5
+Myanmar	BM	92.1	9.6	101.2	28.5
+Namibia	WA	11.7	-29.0	25.3	-17.0
+Nauru	NR	166.8	-0.6	166.9	-0.5
+Navassa Island	BQ	-75.1	18.3	-75.0	18.4
+Nepal	NP	80.0	26.3	88.2	30.4
+Netherlands	NL	3.3	50.7	7.2	53.6
+Netherlands Antilles	NT	-69.2	11.9	-68.2	12.4	-63.3	17.4	-62.9	18.1
+New Caledonia	NC	163.5	-22.8	169.0	-19.5
+New Zealand	NZ	166.4	-48.1	178.6	-34.1
+Nicaragua	NU	-87.7	10.7	-82.6	15.0
+Niger	NG	0.1	11.6	16.0	23.5
+Nigeria	NI	2.6	4.2	14.7	13.9
+Niue	NE	-170.0	-19.2	-169.8	-19.0
+Norfolk Island	NF	168.0	-29.2	168.1	-29.0
+North Korea	KN	124.1	37.5	130.7	43.0
+Northern Mariana Islands	CQ	144.8	14.1	146.1	20.6
+Norway	NO	4.6	57.9	31.1	71.2
+Oman	MU	51.8	16.6	59.8	25.0
+Pacific Ocean	XX	
+Pakistan	PK	60.8	23.6	77.8	37.1
+Palau	PS	132.3	4.3	132.3	4.3	134.1	6.8	134.7	7.7
+Palmyra Atoll	LQ	-162.2	5.8	-162.0	5.9
+Panama	PM	-83.1	7.1	-77.2	9.6
+Papua New Guinea	PP	140.8	-11.7	156.0	-0.9	157.0	-4.9	157.1	-4.8	159.4	-4.7	159.5	-4.5
+Paracel Islands	PF	111.1	15.7	111.2	15.8
+Paraguay	PA	-62.7	-27.7	-54.3	-19.3
+Peru	PE	-81.4	-18.4	-68.7	0.0
+Philippines	RP	116.9	4.9	126.6	21.1
+Pitcairn Islands	PC	-128.4	-24.5	-128.3	-24.3
+Poland	PL	14.1	49.0	24.2	54.8
+Portugal	PO	-9.5	36.9	-6.2	42.1	-31.3	36.9	-25.0	39.8	-17.3	32.4	-16.2	33.2
+Portugal: Azores	XX	-31.3	36.9	-25.0	39.8
+Portugal: Madeira	XX	-17.3	32.4	-16.2	33.2
+Puerto Rico	RQ	-68.0	17.8	-65.2	18.5
+Qatar	QA	50.7	24.4	52.4	26.2
+Republic of the Congo	CF	11.2	-5.1	18.6	3.7
+Reunion	RE	55.2	-21.4	55.8	-20.9
+Romania	RO	20.2	43.6	29.7	48.3
+Russia	RS	-180.0	64.2	-169.0	71.6	19.7	54.3	22.9	55.3	26.9	41.1	180.0	81.3
+Rwanda	RW	28.8	-2.9	30.9	-1.1
+Saint Helena	SH	-5.8	-16.1	-5.6	-15.9
+Saint Kitts and Nevis	SC	62.9	17.0	62.5	17.5
+Saint Lucia	ST	-61.1	13.7	-60.9	14.1
+Saint Pierre and Miquelon	SB	-56.5	46.7	-56.2	47.1
+Saint Vincent and the Grenadines	VC	-61.6	12.4	-61.1	13.4
+Samoa	WS	-172.8	-14.1	-171.4	-13.4
+San Marino	SM	12.4	43.8	12.5	44.0
+Sao Tome and Principe	TP	6.4	0.0	1.7	7.5
+Saudi Arabia	SA	34.4	15.6	55.7	32.2
+Senegal	SG	-17.6	12.3	-11.4	16.7
+Serbia	RB	18.8	41.8	23.1	46.2
+Serbia and Montenegro	YI	
+Seychelles	SE	50.7	-9.6	51.1	-9.2	52.7	-7.2	52.8	-7.0	53.0	-6.3	53.7	-5.1	55.2	-5.9	56.0	-3.7	56.2	-7.2	56.3	-7.1
+Sierra Leone	SL	-13.4	6.9	-10.3	10.0
+Singapore	SN	103.6	1.1	104.1	1.5
+Slovakia	LO	16.8	47.7	22.6	49.6
+Slovenia	SI	13.3	45.4	16.6	46.9
+Solomon Islands	BP	155.5	-11.9	162.8	-5.1	165.6	-11.8	167.0	-10.1	167.1	-10.0	167.3	-9.8	168.8	-12.3	168.8	-12.3
+Somalia	SO	40.9	-1.7	51.4	12.0
+South Africa	SF	16.4	-34.9	32.9	-22.1
+South Georgia and the South Sandwich Islands	SX	-38.3	-54.9	-35.7	-53.9
+South Korea	KS	125.0	33.1	129.6	38.6
+Spain	SP	-9.3	35.1	4.3	43.8	-18.2	27.6	-13.4	29.5
+Spain: Canary Islands	XX	-18.2	27.6	-13.4	29.5
+Spratly Islands	PG	114.0	9.6	115.8	11.1
+Sri Lanka	CE	79.6	5.9	81.9	9.8
+Sudan	SU	21.8	3.4	38.6	23.6
+Suriname	NS	-58.1	1.8	-54.0	6.0
+Svalbard	SV	10.4	76.4	33.5	80.8
+Swaziland	WZ	30.7	-27.4	32.1	-25.7
+Sweden	SW	10.9	55.3	24.2	69.1
+Switzerland	SZ	5.9	45.8	10.5	47.8
+Syria	SY	35.7	32.3	42.4	37.3
+Taiwan	TW	119.3	21.9	122.0	25.3
+Tajikistan	TI	67.3	36.6	75.1	41.0
+Tanzania	TZ	29.3	-11.8	40.4	-1.0
+Thailand	TH	97.3	5.6	105.6	20.5
+Togo	TO	-0.2	6.1	1.8	11.1
+Tokelau	TL	-172.6	-9.5	-171.1	-8.5
+Tonga	TN	-176.3	-22.4	-176.2	-22.3	-175.5	-21.5	-174.5	-20.0
+Trinidad and Tobago	TD	-62.0	10.0	-60.5	11.3
+Tromelin Island	TE	54.5	-15.9	54.5	-15.9
+Tunisia	TS	7.5	30.2	11.6	37.5
+Turkey	TU	25.6	35.8	44.8	42.1
+Turkmenistan	TX	52.4	35.1	66.7	42.8
+Turks and Caicos Islands	TK	-73.8	20.9	-73.0	21.3
+Tuvalu	TV	176.0	-7.3	177.3	-5.6	178.4	-8.0	178.7	-7.4	179.0	-9.5	179.9	-8.5
+Uganda	UG	29.5	-1.5	35.0	4.2
+Ukraine	UP	22.1	44.3	40.2	52.4
+United Arab Emirates	AE	51.1	22.4	56.4	26.1
+United Kingdom	UK	-8.7	49.7	1.8	60.8
+Uruguay	UY	-58.5	-35.0	-53.1	-30.1
+USA	US	-124.8	24.5	-67.0	49.4	-168.2	54.3	-130.0	71.4	172.4	52.3	176.0	53.0	177.2	51.3	179.8	52.1	-179.5	51.0	-172.0	52.5	-171.5	52.0	-164.5	54.5	-164.8	23.5	-164.7	23.6	-162.0	23.0	-161.9	23.1	-160.6	18.9	-154.8	22.2
+USA: Alabama	XX	-88.8	30.1	-84.9	35.0
+USA: Alaska	XX	-168.2	54.3	-130.0	71.4	172.4	52.3	176.0	53.0	177.2	51.3	179.8	52.1	-179.5	51.0	-172.0	52.5	-171.5	52.0	-164.5	54.5
+USA: Alaska, Aleutian Islands	XX	172.4	52.3	176.0	53.0	177.2	51.3	179.8	52.1	-179.5	51.0	-172.0	52.5	-171.5	52.0	-164.5	54.5
+USA: Arizona	XX	-114.9	31.3	-109.0	37.0
+USA: Arkansas	XX	-94.7	33.0	-89.6	36.5
+USA: California	XX	-124.5	32.5	-114.1	42.0
+USA: Colorado	XX	-109.1	36.9	-102.0	41.0
+USA: Connecticut	XX	-73.8	40.9	-71.8	42.1
+USA: Delaware	XX	-75.8	38.4	-74.9	39.8
+USA: Florida	XX	-87.7	24.5	-80.0	31.0
+USA: Georgia	XX	-85.7	30.3	-80.8	35.0
+USA: Hawaii	XX	-164.8	23.5	-164.7	23.6	-162.0	23.0	-161.9	23.1	-160.6	18.9	-154.8	22.2
+USA: Idaho	XX	-117.3	41.9	-111.0	49.0
+USA: Illinois	XX	-91.6	36.9	-87.0	42.5
+USA: Indiana	XX	-88.1	37.7	-84.8	41.8
+USA: Iowa	XX	-96.7	40.3	-90.1	43.5
+USA: Kansas	XX	-102.1	36.9	-94.6	40.0
+USA: Kentucky	XX	-89.5	36.5	-82.0	39.1
+USA: Louisiana	XX	-94.1	28.9	-88.8	33.0
+USA: Maine	XX	-71.1	43.0	-67.0	47.5
+USA: Maryland	XX	-79.5	37.8	-75.1	39.7
+USA: Massachusetts	XX	-73.6	41.2	-69.9	42.9
+USA: Michigan	XX	-90.5	41.6	-82.1	48.3
+USA: Minnesota	XX	-97.3	43.4	-90.0	49.4
+USA: Mississippi	XX	-91.7	30.1	-88.1	35.0
+USA: Missouri	XX	-95.8	36.0	-89.1	40.6
+USA: Montana	XX	-116.1	44.3	-104.0	49.0
+USA: Nebraska	XX	-104.1	40.0	-95.3	43.0
+USA: Nevada	XX	-120.0	35.0	-114.0	42.0
+USA: New Hampshire	XX	-72.6	42.6	-70.7	45.3
+USA: New Jersey	XX	-75.6	38.9	-73.9	41.4
+USA: New Mexico	XX	-109.1	31.3	-103.0	37.0
+USA: New York	XX	-79.8	40.4	-71.9	45.0
+USA: North Carolina	XX	-84.4	33.8	-75.5	36.6
+USA: North Dakota	XX	-104.1	45.9	-96.6	49.0
+USA: Ohio	XX	-84.9	38.3	-80.5	42.3
+USA: Oklahoma	XX	-103.1	33.6	-94.4	37.0
+USA: Oregon	XX	-124.6	41.9	-116.5	46.3
+USA: Pennsylvania	XX	-80.6	39.7	-74.7	42.5
+USA: Rhode Island	XX	-71.9	41.1	-71.1	42.0
+USA: South Carolina	XX	-83.4	32.0	-78.6	35.2
+USA: South Dakota	XX	-104.1	42.4	-96.4	45.9
+USA: Tennessee	XX	-90.4	35.0	-81.7	36.7
+USA: Texas	XX	-106.7	25.8	-93.5	36.5
+USA: Utah	XX	-114.1	37.0	-109.1	42.0
+USA: Vermont	XX	-73.5	42.7	-71.5	45.0
+USA: Virginia	XX	-83.7	36.5	-75.2	39.5
+USA: Washington	XX	-124.8	45.5	-116.9	49.0
+USA: West Virginia	XX	-82.7	37.1	-77.7	40.6
+USA: Wisconsin	XX	-92.9	42.4	-86.3	47.3
+USA: Wyoming	XX	-111.1	40.9	-104.1	45.0
+Uzbekistan	UZ	55.9	37.1	73.1	45.6
+Vanuatu	NH	166.5	-20.3	170.2	-13.1
+Venezuela	VE	-73.4	0.7	-59.8	12.2
+Viet Nam	VM	102.1	8.4	109.5	23.4
+Virgin Islands	VQ	-65.1	17.6	-64.6	18.5
+Wake Island	WQ	166.5	19.2	166.7	19.3
+Wallis and Futuna	WF	-178.3	-14.4	-178.0	-14.2	-176.3	-13.4	-176.1	-13.2
+West Bank	WE	34.8	31.3	35.6	32.6
+Western Sahara	WI	-17.2	20.7	-8.7	27.7
+Yemen	YM	41.8	11.7	54.5	19.0
+Yugoslavia	XX	13.3	40.8	23.0	46.9
+Zambia	ZA	21.9	-18.1	33.7	-8.2
+Zimbabwe	ZI	25.2	-22.5	33.1	-15.6
diff --git a/data/ecnum_ambiguous.txt b/data/ecnum_ambiguous.txt
index 51dd95a9..4934c8a5 100644
--- a/data/ecnum_ambiguous.txt
+++ b/data/ecnum_ambiguous.txt
@@ -410,6 +410,7 @@
 3.4.24.n
 3.4.25.-
 3.4.25.n
+3.4.99.-
 3.4.n.n
 3.5.-.-
 3.5.1.-
diff --git a/data/ecnum_deleted.txt b/data/ecnum_deleted.txt
new file mode 100644
index 00000000..8164888b
--- /dev/null
+++ b/data/ecnum_deleted.txt
@@ -0,0 +1,156 @@
+1.1.1.74
+1.1.1.155
+1.1.1.249
+1.1.3.25
+1.1.3.31
+1.1.5.1
+1.2.1.6
+1.2.3.10
+1.2.7.9
+1.3.1.23
+1.3.1.55
+1.3.1.59
+1.4.3.18
+1.5.3.3
+1.6.2.3
+1.6.5.1
+1.7.1.8
+1.7.99.2
+1.7.99.5
+1.8.1.1
+1.12.99.2
+1.12.99.5
+1.13.1.7
+1.13.11.7
+1.13.11.42
+1.13.12.10
+1.13.12.11
+1.14.1.9
+1.14.1.11
+1.14.11.5
+1.14.13.65
+1.14.14.4
+1.14.99.18
+1.99.1.3
+1.99.1.4
+1.99.1.6
+1.99.1.8
+1.99.1.10
+1.99.1.12
+2.1.1.30
+2.1.1.73
+2.1.1.138
+2.1.3.4
+2.3.1.120
+2.3.1.124
+2.4.1.6
+2.4.1.75
+2.4.1.112
+2.4.1.154
+2.4.1.233
+2.4.1.235
+2.6.1.20
+2.6.1.61
+2.6.1.69
+2.7.1.9
+2.7.1.57
+2.7.1.70
+2.7.1.97
+2.7.1.98
+2.7.1.120
+2.7.7.20
+2.7.7.29
+2.8.2.12
+2.8.3.4
+3.1.1.9
+3.1.1.16
+3.1.2.9
+3.1.3.61
+3.1.4.24
+3.1.4.26
+3.1.4.29
+3.1.4.32
+3.1.4.33
+3.1.4.34
+3.1.6.5
+3.2.1.5
+3.2.1.9
+3.2.1.16
+3.2.1.19
+3.2.1.27
+3.2.1.90
+3.4.4.25
+3.4.11.11
+3.4.11.12
+3.4.12.9
+3.4.12.13
+3.4.13.14
+3.4.13.16
+3.4.14.7
+3.4.17.5
+3.4.19.4
+3.4.21.16
+3.4.21.17
+3.4.21.18
+3.4.21.23
+3.4.21.24
+3.4.21.33
+3.4.21.40
+3.4.21.51
+3.4.21.52
+3.4.21.56
+3.4.21.58
+3.4.22.13
+3.4.22.20
+3.4.23.11
+3.4.23.13
+3.4.23.14
+3.4.24.2
+3.4.24.9
+3.4.24.10
+3.4.99.2
+3.4.99.3
+3.4.99.7
+3.4.99.8
+3.4.99.9
+3.4.99.11
+3.4.99.12
+3.4.99.14
+3.4.99.15
+3.4.99.16
+3.4.99.17
+3.4.99.18
+3.4.99.20
+3.4.99.21
+3.4.99.23
+3.4.99.24
+3.4.99.27
+3.4.99.29
+3.4.99.33
+3.4.99.34
+3.4.99.37
+3.4.99.39
+3.4.99.40
+3.4.99.42
+3.5.1.80
+3.6.3.13
+3.6.3.45
+3.13.1.2
+4.1.1.13
+4.1.2.3
+4.1.2.6
+4.2.1.23
+4.2.1.71
+4.2.1.86
+4.2.99.5
+4.3.1.21
+4.4.1.12
+5.2.1.11
+5.3.1.2
+5.3.1.11
+5.3.1.18
+5.3.99.1
+5.4.3.1
+6.1.1.8
+6.2.1.29
+6.3.2.15
diff --git a/data/ecnum_replaced.txt b/data/ecnum_replaced.txt
new file mode 100644
index 00000000..fdb92a1f
--- /dev/null
+++ b/data/ecnum_replaced.txt
@@ -0,0 +1,576 @@
+1.1.1.68	1.5.1.20
+1.1.1.70	1.2.1.3
+1.1.1.89	1.1.1.86
+1.1.1.109	1.3.1.28
+1.1.1.139	1.1.1.21
+1.1.1.171	1.5.1.20
+1.1.1.180	1.1.1.131
+1.1.1.182	1.1.1.228
+1.1.1.204	1.17.1.4
+1.1.1.242	1.3.1.69
+1.1.1.253	1.5.1.33
+1.1.2.1	1.1.99.5
+1.1.3.1	1.1.3.15
+1.1.3.2	1.13.12.4
+1.1.3.22	1.17.3.2
+1.1.3.24	1.3.3.12
+1.1.3.26	1.21.3.2
+1.1.3.32	1.14.21.1
+1.1.3.33	1.14.21.2
+1.1.3.34	1.14.21.3
+1.1.3.35	1.14.21.4
+1.1.3.36	1.14.21.5
+1.1.99.15	1.5.1.20
+1.1.99.17	1.1.5.2
+1.1.99.19	1.17.99.4
+1.2.1.1	1.1.1.284
+1.2.1.14	1.1.1.205
+1.2.1.34	1.1.1.131
+1.2.1.35	1.1.1.203
+1.2.1.37	1.17.1.4
+1.2.1.55	1.1.1.279
+1.2.1.56	1.1.1.280
+1.2.3.2	1.17.3.2
+1.2.3.12	1.14.13.82
+1.2.4.3	1.2.4.4
+1.2.99.1	1.17.99.4
+1.3.1.50	1.1.1.252
+1.3.2.1	1.3.99.2
+1.3.2.2	1.3.99.3
+1.3.3.2	1.14.21.6
+1.3.99.9	1.21.99.1
+1.4.1.6	1.21.4.1
+1.4.3.9	1.4.3.4
+1.4.3.17	1.3.3.10
+1.4.4.1	1.21.4.1
+1.5.1.4	1.5.1.3
+1.5.1.13	1.17.1.5
+1.5.1.14	1.5.1.21
+1.5.3.8	1.3.3.8
+1.5.3.9	1.21.3.3
+1.5.99.7	1.5.8.2
+1.5.99.10	1.5.8.1
+1.6.2.1	1.6.99.3
+1.6.4.1	1.8.1.6
+1.6.4.2	1.8.1.7
+1.6.4.3	1.8.1.4
+1.6.4.4	1.8.1.8
+1.6.4.5	1.8.1.9
+1.6.4.6	1.8.1.10
+1.6.4.7	1.8.1.11
+1.6.4.8	1.8.1.12
+1.6.4.9	1.8.1.13
+1.6.4.10	1.8.1.14
+1.6.6.1	1.7.1.1
+1.6.6.2	1.7.1.2
+1.6.6.3	1.7.1.3
+1.6.6.4	1.7.1.4
+1.6.6.5	1.7.2.1
+1.6.6.6	1.7.1.5
+1.6.6.7	1.7.1.6
+1.6.6.8	1.7.1.7
+1.6.6.10	1.7.1.9
+1.6.6.11	1.7.1.10
+1.6.6.12	1.7.1.11
+1.6.6.13	1.7.1.12
+1.6.7.1	1.18.1.2
+1.6.7.2	1.18.1.1
+1.6.8.1	1.5.1.29
+1.6.8.2	1.5.1.30
+1.6.99.2	1.6.5.2
+1.6.99.4	1.18.1.2
+1.6.99.7	1.5.1.34
+1.6.99.8	1.16.1.3
+1.6.99.9	1.16.1.4
+1.6.99.10	1.5.1.34
+1.6.99.11	1.16.1.5
+1.6.99.12	1.16.1.6
+1.6.99.13	1.16.1.7
+1.7.99.3	1.7.2.1
+1.8.4.5	1.8.4.13
+1.8.4.6	1.8.4.11
+1.8.6.1	2.5.1.18
+1.8.99.4	1.8.4.8
+1.9.3.2	1.7.2.1
+1.10.3.7	1.21.3.4
+1.10.3.8	1.21.3.5
+1.11.1.4	1.13.11.11
+1.12.1.1	1.12.7.2
+1.12.7.1	1.12.7.2
+1.12.99.1	1.12.98.1
+1.12.99.3	1.12.5.1
+1.12.99.4	1.12.98.2
+1.13.1.1	1.13.11.1
+1.13.1.2	1.13.11.2
+1.13.1.3	1.13.11.3
+1.13.1.4	1.13.11.4
+1.13.1.5	1.13.11.5
+1.13.1.6	1.13.11.6
+1.13.1.8	1.13.11.8
+1.13.1.9	1.13.11.9
+1.13.1.10	1.13.11.10
+1.13.1.11	1.13.99.1
+1.13.1.12	1.13.11.11
+1.13.1.13	1.13.11.12
+1.13.11.21	1.14.99.36
+1.13.99.2	1.14.12.10
+1.13.99.4	1.14.12.9
+1.13.99.5	1.13.11.47
+1.14.1.1	1.14.14.1
+1.14.1.2	1.14.13.9
+1.14.1.3	1.14.99.7
+1.14.1.4	1.14.99.2
+1.14.1.5	1.14.13.5
+1.14.1.6	1.14.15.4
+1.14.1.7	1.14.99.9
+1.14.1.8	1.14.99.10
+1.14.1.10	1.14.99.11
+1.14.2.1	1.14.17.1
+1.14.2.2	1.13.11.27
+1.14.3.1	1.14.16.1
+1.14.12.2	1.14.13.35
+1.14.12.6	1.14.13.66
+1.14.13.45	1.14.18.2
+1.14.14.2	1.14.14.1
+1.14.17.2	1.14.18.1
+1.14.99.5	1.14.19.1
+1.14.99.6	1.14.19.2
+1.14.99.8	1.14.14.1
+1.14.99.13	1.14.13.23
+1.14.99.16	1.14.13.72
+1.14.99.17	1.14.16.5
+1.14.99.25	1.14.19.3
+1.17.1.6	1.17.99.5
+1.18.2.1	1.18.6.1
+1.18.3.1	1.12.7.2
+1.18.96.1	1.15.1.2
+1.18.99.1	1.12.7.2
+1.97.1.5	1.20.4.1
+1.97.1.6	1.20.99.1
+1.97.1.7	1.20.4.2
+1.98.1.1	1.12.7.2
+1.99.1.1	1.14.14.1
+1.99.1.2	1.14.16.1
+1.99.1.5	1.14.13.9
+1.99.1.7	1.14.15.4
+1.99.1.9	1.14.99.9
+1.99.1.11	1.14.99.10
+1.99.1.13	1.14.99.7
+1.99.1.14	1.13.11.27
+1.99.2.1	1.13.11.12
+1.99.2.2	1.13.11.1
+1.99.2.3	1.13.11.3
+1.99.2.4	1.13.11.4
+1.99.2.5	1.13.11.5
+1.99.2.6	1.13.99.1
+2.1.1.23	2.1.1.126
+2.1.1.24	2.1.1.100
+2.1.1.58	2.6.1.5
+2.1.1.81	2.1.1.49
+2.1.1.134	2.1.1.129
+2.1.1.135	1.16.1.8
+2.1.2.6	2.1.2.5
+2.1.2.12	2.1.1.74
+2.3.1.55	2.3.1.82
+2.4.1.3	2.4.1.25
+2.4.1.42	2.4.1.17
+2.4.1.51	2.4.1.145
+2.4.1.55	2.7.8.14
+2.4.1.59	2.4.1.17
+2.4.1.61	2.4.1.17
+2.4.1.72	2.4.2.24
+2.4.1.76	2.4.1.17
+2.4.1.77	2.4.1.17
+2.4.1.84	2.4.1.17
+2.4.1.89	2.4.1.69
+2.4.1.93	4.2.2.18
+2.4.1.98	2.4.1.90
+2.4.1.107	2.4.1.17
+2.4.1.108	2.4.1.17
+2.4.1.124	2.4.1.87
+2.4.1.151	2.4.1.87
+2.4.1.169	2.4.2.39
+2.4.1.200	4.2.2.17
+2.4.1.204	2.4.2.40
+2.4.2.13	2.5.1.6
+2.5.1.12	2.5.1.18
+2.5.1.13	2.5.1.18
+2.5.1.14	2.5.1.18
+2.5.1.37	4.4.1.20
+2.5.1.40	4.2.3.9
+2.6.1.10	2.6.1.21
+2.6.1.25	2.6.1.24
+2.6.1.53	1.4.1.13
+2.6.2.1	2.1.4.1
+2.7.1.37	2.7.11.1
+2.7.1.38	2.7.11.19
+2.7.1.75	2.7.1.21
+2.7.1.96	2.7.1.86
+2.7.1.99	2.7.11.2
+2.7.1.104	2.7.99.1
+2.7.1.109	2.7.11.31
+2.7.1.110	2.7.11.3
+2.7.1.111	2.7.11.27
+2.7.1.112	2.7.10.1
+2.7.1.115	2.7.11.4
+2.7.1.116	2.7.11.5
+2.7.1.117	2.7.11.18
+2.7.1.123	2.7.11.17
+2.7.1.124	2.7.11.6
+2.7.1.125	2.7.11.14
+2.7.1.126	2.7.11.15
+2.7.1.128	2.7.11.27
+2.7.1.129	2.7.11.7
+2.7.1.131	2.7.11.29
+2.7.1.132	2.7.11.28
+2.7.1.133	2.7.1.134
+2.7.1.135	2.7.11.26
+2.7.1.139	2.7.1.134
+2.7.1.141	2.7.11.23
+2.7.1.152	2.7.4.21
+2.7.2.5	6.3.4.16
+2.7.2.9	6.3.5.5
+2.7.3.11	2.7.13.1
+2.7.3.12	2.7.13.2
+2.7.4.5	2.7.4.14
+2.7.5.1	5.4.2.2
+2.7.5.2	5.4.2.3
+2.7.5.3	5.4.2.1
+2.7.5.4	5.4.2.4
+2.7.5.5	5.4.2.5
+2.7.5.6	5.4.2.7
+2.7.5.7	5.4.2.8
+2.7.7.16	3.1.27.5
+2.7.7.17	3.1.27.1
+2.7.7.26	3.1.27.3
+2.7.8.16	2.7.8.2
+3.1.1.12	3.1.1.1
+3.1.1.18	3.1.1.17
+3.1.1.62	3.5.1.47
+3.1.1.69	3.5.1.89
+3.1.2.8	3.1.2.6
+3.1.2.24	3.13.1.3
+3.1.3.30	3.1.3.7
+3.1.3.65	3.1.3.64
+3.1.4.5	3.1.21.1
+3.1.4.6	3.1.22.1
+3.1.4.7	3.1.31.1
+3.1.4.8	3.1.27.3
+3.1.4.9	3.1.30.2
+3.1.4.10	4.6.1.13
+3.1.4.18	3.1.16.1
+3.1.4.19	3.1.13.3
+3.1.4.20	3.1.13.1
+3.1.4.21	3.1.30.1
+3.1.4.22	3.1.27.5
+3.1.4.23	3.1.27.1
+3.1.4.25	3.1.11.1
+3.1.4.27	3.1.11.2
+3.1.4.28	3.1.11.3
+3.1.4.30	3.1.21.2
+3.1.4.31	3.1.11.4
+3.1.4.36	3.1.4.43
+3.1.4.47	4.6.1.14
+3.1.22.3	3.1.21.7
+3.1.23.1	3.1.21.4
+3.1.23.2	3.1.21.4
+3.1.23.3	3.1.21.4
+3.1.23.4	3.1.21.4
+3.1.23.5	3.1.21.4
+3.1.23.6	3.1.21.4
+3.1.23.7	3.1.21.4
+3.1.23.8	3.1.21.4
+3.1.23.9	3.1.21.4
+3.1.23.10	3.1.21.4
+3.1.23.11	3.1.21.4
+3.1.23.12	3.1.21.4
+3.1.23.13	3.1.21.4
+3.1.23.14	3.1.21.4
+3.1.23.15	3.1.21.4
+3.1.23.16	3.1.21.4
+3.1.23.17	3.1.21.4
+3.1.23.18	3.1.21.4
+3.1.23.19	3.1.21.4
+3.1.23.20	3.1.21.4
+3.1.23.21	3.1.21.4
+3.1.23.22	3.1.21.4
+3.1.23.23	3.1.21.4
+3.1.23.24	3.1.21.4
+3.1.23.25	3.1.21.4
+3.1.23.26	3.1.21.4
+3.1.23.27	3.1.21.4
+3.1.23.28	3.1.21.4
+3.1.23.29	3.1.21.4
+3.1.23.30	3.1.21.4
+3.1.23.31	3.1.21.4
+3.1.23.32	3.1.21.4
+3.1.23.33	3.1.21.4
+3.1.23.34	3.1.21.4
+3.1.23.35	3.1.21.4
+3.1.23.36	3.1.21.4
+3.1.23.37	3.1.21.4
+3.1.23.38	3.1.21.4
+3.1.23.39	3.1.21.4
+3.1.23.40	3.1.21.4
+3.1.23.41	3.1.21.4
+3.1.23.42	3.1.21.4
+3.1.23.43	3.1.21.4
+3.1.23.44	3.1.21.4
+3.1.23.45	3.1.21.4
+3.1.23.46	3.1.21.4
+3.1.23.47	3.1.21.4
+3.1.23.48	3.1.21.4
+3.1.23.49	3.1.21.4
+3.1.23.50	3.1.21.4
+3.1.23.51	3.1.21.4
+3.1.23.52	3.1.21.4
+3.1.23.53	3.1.21.4
+3.1.23.54	3.1.21.4
+3.1.23.55	3.1.21.4
+3.1.23.56	3.1.21.4
+3.1.23.57	3.1.21.4
+3.1.23.58	3.1.21.4
+3.1.23.59	3.1.21.4
+3.1.24.1	3.1.21.3
+3.1.24.2	3.1.21.3
+3.1.24.3	3.1.21.5
+3.1.24.4	3.1.21.5
+3.1.25.2	4.2.99.18
+3.2.1.12	3.2.1.54
+3.2.1.13	3.2.1.54
+3.2.1.29	3.2.1.52
+3.2.1.30	3.2.1.52
+3.2.1.34	3.2.1.35
+3.2.1.69	3.2.1.41
+3.2.1.79	3.2.1.55
+3.2.1.138	4.2.2.15
+3.2.1.148	4.4.1.21
+3.2.2.18	3.5.1.52
+3.2.3.1	3.2.1.147
+3.3.1.3	4.4.1.21
+3.3.2.3	3.3.2.9
+3.4.1.1	3.4.11.1
+3.4.1.2	3.4.11.2
+3.4.1.3	3.4.11.4
+3.4.1.4	3.4.11.5
+3.4.2.1	3.4.17.1
+3.4.2.2	3.4.17.2
+3.4.2.3	3.4.17.4
+3.4.3.1	3.4.13.18
+3.4.3.2	3.4.13.18
+3.4.3.3	3.4.13.3
+3.4.3.4	3.4.13.5
+3.4.3.5	3.4.11.2
+3.4.3.6	3.4.13.18
+3.4.3.7	3.4.13.9
+3.4.4.1	3.4.23.1
+3.4.4.2	3.4.23.2
+3.4.4.3	3.4.23.4
+3.4.4.4	3.4.21.4
+3.4.4.5	3.4.21.1
+3.4.4.6	3.4.21.1
+3.4.4.7	3.4.21.36
+3.4.4.8	3.4.21.9
+3.4.4.9	3.4.14.1
+3.4.4.10	3.4.22.2
+3.4.4.11	3.4.22.6
+3.4.4.12	3.4.22.3
+3.4.4.13	3.4.21.5
+3.4.4.14	3.4.21.7
+3.4.4.15	3.4.23.15
+3.4.4.16	3.4.21.62
+3.4.4.17	3.4.23.20
+3.4.4.18	3.4.22.10
+3.4.4.19	3.4.24.3
+3.4.4.20	3.4.22.8
+3.4.4.21	3.4.21.34
+3.4.4.22	3.4.23.3
+3.4.4.23	3.4.23.5
+3.4.4.24	3.4.22.32
+3.4.11.8	3.4.19.3
+3.4.12.1	3.4.16.5
+3.4.12.2	3.4.17.1
+3.4.12.3	3.4.17.2
+3.4.12.4	3.4.16.2
+3.4.12.5	3.5.1.28
+3.4.12.6	3.4.17.8
+3.4.12.7	3.4.17.3
+3.4.12.8	3.4.17.4
+3.4.12.10	3.4.19.9
+3.4.12.11	3.4.17.6
+3.4.12.12	3.4.16.5
+3.4.13.1	3.4.13.18
+3.4.13.2	3.4.13.18
+3.4.13.6	3.4.11.2
+3.4.13.8	3.4.13.18
+3.4.13.10	3.4.19.5
+3.4.13.11	3.4.13.18
+3.4.13.13	3.4.13.3
+3.4.13.15	3.4.13.18
+3.4.14.3	3.4.19.1
+3.4.14.8	3.4.14.9
+3.4.15.2	3.4.19.2
+3.4.15.3	3.4.15.5
+3.4.16.1	3.4.16.5
+3.4.16.3	3.4.16.5
+3.4.17.7	3.5.1.28
+3.4.17.9	3.4.17.4
+3.4.19.8	3.4.17.21
+3.4.19.10	3.5.1.28
+3.4.21.8	3.4.21.35
+3.4.21.11	3.4.21.36
+3.4.21.13	3.4.16.5
+3.4.21.14	3.4.21.62
+3.4.21.15	3.4.21.63
+3.4.21.28	3.4.21.74
+3.4.21.29	3.4.21.74
+3.4.21.30	3.4.21.74
+3.4.21.31	3.4.21.68
+3.4.21.44	3.4.21.43
+3.4.21.87	3.4.23.49
+3.4.22.4	3.4.22.32
+3.4.22.5	3.4.22.33
+3.4.22.9	3.4.21.48
+3.4.22.11	3.4.24.56
+3.4.22.12	3.4.19.9
+3.4.22.17	3.4.22.52
+3.4.22.18	3.4.21.26
+3.4.22.19	3.4.24.15
+3.4.22.21	3.4.25.1
+3.4.22.22	3.4.24.37
+3.4.22.23	3.4.21.61
+3.4.23.6	3.4.23.18
+3.4.23.7	3.4.23.20
+3.4.23.8	3.4.23.25
+3.4.23.9	3.4.23.21
+3.4.23.10	3.4.23.22
+3.4.23.27	3.4.21.103
+3.4.23.33	3.4.21.101
+3.4.23.37	3.4.21.100
+3.4.24.4	3.4.24.25
+3.4.24.5	3.4.25.1
+3.4.24.8	3.4.24.3
+3.4.99.1	3.4.23.28
+3.4.99.4	3.4.23.12
+3.4.99.5	3.4.24.3
+3.4.99.6	3.4.24.21
+3.4.99.10	3.4.24.56
+3.4.99.13	3.4.24.32
+3.4.99.19	3.4.23.15
+3.4.99.22	3.4.24.29
+3.4.99.25	3.4.23.21
+3.4.99.26	3.4.21.73
+3.4.99.28	3.4.21.60
+3.4.99.30	3.4.24.20
+3.4.99.31	3.4.24.15
+3.4.99.32	3.4.24.20
+3.4.99.35	3.4.23.36
+3.4.99.36	3.4.21.89
+3.4.99.38	3.4.23.17
+3.4.99.41	3.4.24.64
+3.4.99.43	3.4.23.42
+3.4.99.44	3.4.24.55
+3.4.99.45	3.4.24.56
+3.4.99.46	3.4.25.1
+3.5.1.34	3.4.13.5
+3.5.1.37	3.5.1.26
+3.5.1.45	6.3.4.6
+3.5.2.8	3.5.2.6
+3.5.5.3	4.2.1.104
+3.6.1.4	3.6.1.3
+3.6.1.32	3.6.4.1
+3.6.1.33	3.6.4.2
+3.6.1.34	3.6.3.14
+3.6.1.35	3.6.3.6
+3.6.1.36	3.6.3.10
+3.6.1.37	3.6.3.9
+3.6.1.38	3.6.3.8
+3.6.1.46	3.6.5.1
+3.6.1.47	3.6.5.2
+3.6.1.48	3.6.5.3
+3.6.1.49	3.6.5.4
+3.6.1.50	3.6.5.5
+3.6.1.51	3.6.5.6
+3.8.1.4	1.97.1.10
+3.8.2.1	3.1.8.2
+4.1.1.10	4.1.1.12
+4.1.1.26	4.1.1.28
+4.1.1.27	4.1.1.28
+4.1.2.1	4.1.3.16
+4.1.2.7	4.1.2.13
+4.1.2.15	2.5.1.54
+4.1.2.16	2.5.1.55
+4.1.2.31	4.1.3.16
+4.1.3.2	2.3.3.9
+4.1.3.5	2.3.3.10
+4.1.3.7	2.3.3.1
+4.1.3.8	2.3.3.8
+4.1.3.9	2.3.3.11
+4.1.3.10	2.3.3.7
+4.1.3.11	2.3.3.12
+4.1.3.12	2.3.3.13
+4.1.3.15	2.2.1.5
+4.1.3.18	2.2.1.6
+4.1.3.19	2.5.1.56
+4.1.3.20	2.5.1.57
+4.1.3.21	2.3.3.14
+4.1.3.23	2.3.3.2
+4.1.3.28	2.3.3.3
+4.1.3.29	2.3.3.4
+4.1.3.31	2.3.3.5
+4.1.3.33	2.3.3.6
+4.1.3.37	2.2.1.7
+4.1.99.4	3.5.99.7
+4.1.99.6	4.2.3.6
+4.1.99.7	4.2.3.9
+4.1.99.8	4.2.3.14
+4.1.99.9	4.2.3.15
+4.1.99.10	4.2.3.16
+4.2.1.13	4.3.1.17
+4.2.1.14	4.3.1.18
+4.2.1.15	4.4.1.1
+4.2.1.16	4.3.1.19
+4.2.1.21	4.2.1.22
+4.2.1.26	4.3.1.9
+4.2.1.29	4.99.1.6
+4.2.1.37	3.3.2.4
+4.2.1.38	4.3.1.20
+4.2.1.63	3.3.2.9
+4.2.1.64	3.3.2.9
+4.2.1.72	4.1.1.78
+4.2.1.102	4.2.1.100
+4.2.2.4	4.2.2.20
+4.2.99.1	4.2.2.1
+4.2.99.2	4.2.3.1
+4.2.99.3	4.2.2.2
+4.2.99.4	4.2.2.3
+4.2.99.6	4.2.2.5
+4.2.99.7	4.2.3.2
+4.2.99.8	2.5.1.47
+4.2.99.9	2.5.1.48
+4.2.99.10	2.5.1.49
+4.2.99.11	4.2.3.3
+4.2.99.13	2.5.1.50
+4.2.99.14	2.5.1.51
+4.2.99.15	2.5.1.52
+4.2.99.16	2.5.1.53
+4.2.99.17	2.5.1.51
+4.2.99.19	4.4.1.23
+4.3.1.8	2.5.1.61
+4.3.99.1	4.2.1.104
+4.4.1.7	2.5.1.18
+4.4.1.18	1.8.3.5
+4.6.1.3	4.2.3.4
+4.6.1.4	4.2.3.5
+4.6.1.5	4.2.3.7
+4.6.1.7	4.2.3.8
+4.6.1.8	4.2.3.10
+4.6.1.9	4.2.3.11
+4.6.1.10	4.2.3.12
+4.6.1.11	4.2.3.13
+5.3.1.10	3.5.99.6
+5.3.1.19	2.6.1.16
+5.4.99.6	5.4.4.2
+5.4.99.10	5.4.99.11
+6.2.1.21	6.2.1.30
+6.3.1.3	6.3.4.13
diff --git a/data/ecnum_specific.txt b/data/ecnum_specific.txt
index 92304422..2de6d9e1 100644
--- a/data/ecnum_specific.txt
+++ b/data/ecnum_specific.txt
@@ -274,6 +274,7 @@
 1.1.1.288
 1.1.1.289
 1.1.1.290
+1.1.1.291
 1.1.2.2
 1.1.2.3
 1.1.2.4
@@ -298,7 +299,6 @@
 1.1.3.20
 1.1.3.21
 1.1.3.23
-1.1.3.24
 1.1.3.27
 1.1.3.28
 1.1.3.29
@@ -338,6 +338,7 @@
 1.1.99.28
 1.1.99.29
 1.1.99.30
+1.1.99.31
 1.2.1.2
 1.2.1.3
 1.2.1.4
@@ -489,7 +490,6 @@
 1.3.1.56
 1.3.1.57
 1.3.1.58
-1.3.1.59
 1.3.1.60
 1.3.1.61
 1.3.1.62
@@ -521,6 +521,7 @@
 1.3.3.9
 1.3.3.10
 1.3.3.11
+1.3.3.12
 1.3.5.1
 1.3.7.1
 1.3.7.2
@@ -586,6 +587,7 @@
 1.4.3.15
 1.4.3.16
 1.4.3.19
+1.4.3.20
 1.4.4.2
 1.4.7.1
 1.4.99.1
@@ -624,6 +626,7 @@
 1.5.1.32
 1.5.1.33
 1.5.1.34
+1.5.1.35
 1.5.3.1
 1.5.3.2
 1.5.3.4
@@ -718,12 +721,14 @@
 1.8.4.2
 1.8.4.3
 1.8.4.4
-1.8.4.5
-1.8.4.6
 1.8.4.7
 1.8.4.8
 1.8.4.9
 1.8.4.10
+1.8.4.11
+1.8.4.12
+1.8.4.13
+1.8.4.14
 1.8.5.1
 1.8.5.2
 1.8.7.1
@@ -832,7 +837,6 @@
 1.13.12.7
 1.13.12.8
 1.13.12.9
-1.13.12.11
 1.13.12.12
 1.13.12.13
 1.13.12.14
@@ -863,6 +867,8 @@
 1.14.11.24
 1.14.11.25
 1.14.11.26
+1.14.11.27
+1.14.11.28
 1.14.12.1
 1.14.12.3
 1.14.12.4
@@ -1057,7 +1063,6 @@
 1.17.1.3
 1.17.1.4
 1.17.1.5
-1.17.1.6
 1.17.3.1
 1.17.3.2
 1.17.3.3
@@ -1069,6 +1074,7 @@
 1.17.99.2
 1.17.99.3
 1.17.99.4
+1.17.99.5
 1.18.1.1
 1.18.1.2
 1.18.1.3
@@ -1617,7 +1623,6 @@
 2.4.1.150
 2.4.1.152
 2.4.1.153
-2.4.1.154
 2.4.1.155
 2.4.1.156
 2.4.1.157
@@ -1694,7 +1699,6 @@
 2.4.1.231
 2.4.1.232
 2.4.1.234
-2.4.1.235
 2.4.1.236
 2.4.1.237
 2.4.1.238
@@ -1890,6 +1894,8 @@
 2.6.1.79
 2.6.1.80
 2.6.1.81
+2.6.1.82
+2.6.1.83
 2.6.3.1
 2.6.99.1
 2.6.99.2
@@ -2020,6 +2026,7 @@
 2.7.1.157
 2.7.1.158
 2.7.1.159
+2.7.1.160
 2.7.2.1
 2.7.2.2
 2.7.2.3
@@ -2064,6 +2071,7 @@
 2.7.4.20
 2.7.4.21
 2.7.4.22
+2.7.4.23
 2.7.6.1
 2.7.6.2
 2.7.6.3
@@ -2127,6 +2135,7 @@
 2.7.7.61
 2.7.7.62
 2.7.7.63
+2.7.7.64
 2.7.8.1
 2.7.8.2
 2.7.8.3
@@ -2152,6 +2161,7 @@
 2.7.8.24
 2.7.8.25
 2.7.8.26
+2.7.8.27
 2.7.9.1
 2.7.9.2
 2.7.9.3
@@ -2328,6 +2338,7 @@
 3.1.1.77
 3.1.1.78
 3.1.1.79
+3.1.1.80
 3.1.2.1
 3.1.2.2
 3.1.2.3
@@ -2425,6 +2436,7 @@
 3.1.3.74
 3.1.3.75
 3.1.3.76
+3.1.3.77
 3.1.4.1
 3.1.4.2
 3.1.4.3
@@ -2663,6 +2675,7 @@
 3.2.1.152
 3.2.1.153
 3.2.1.154
+3.2.1.155
 3.2.1.156
 3.2.1.157
 3.2.1.158
@@ -2735,6 +2748,7 @@
 3.4.13.19
 3.4.13.20
 3.4.13.21
+3.4.13.22
 3.4.14.1
 3.4.14.2
 3.4.14.4
@@ -2743,6 +2757,7 @@
 3.4.14.9
 3.4.14.10
 3.4.14.11
+3.4.14.12
 3.4.15.1
 3.4.15.4
 3.4.15.5
@@ -2862,6 +2877,20 @@
 3.4.21.103
 3.4.21.104
 3.4.21.105
+3.4.21.106
+3.4.21.107
+3.4.21.108
+3.4.21.109
+3.4.21.110
+3.4.21.111
+3.4.21.112
+3.4.21.113
+3.4.21.114
+3.4.21.115
+3.4.21.116
+3.4.21.117
+3.4.21.118
+3.4.21.119
 3.4.22.1
 3.4.22.2
 3.4.22.3
@@ -3129,6 +3158,7 @@
 3.5.2.15
 3.5.2.16
 3.5.2.17
+3.5.2.18
 3.5.3.1
 3.5.3.2
 3.5.3.3
@@ -3565,10 +3595,12 @@
 4.2.1.106
 4.2.1.107
 4.2.1.108
+4.2.1.109
+4.2.1.110
+4.2.1.111
 4.2.2.1
 4.2.2.2
 4.2.2.3
-4.2.2.4
 4.2.2.5
 4.2.2.6
 4.2.2.7
@@ -3584,6 +3616,8 @@
 4.2.2.17
 4.2.2.18
 4.2.2.19
+4.2.2.20
+4.2.2.21
 4.2.3.1
 4.2.3.2
 4.2.3.3
@@ -3777,6 +3811,7 @@
 5.3.3.12
 5.3.3.13
 5.3.3.14
+5.3.3.15
 5.3.4.1
 5.3.99.2
 5.3.99.3
@@ -3906,6 +3941,7 @@
 6.3.1.9
 6.3.1.10
 6.3.1.11
+6.3.1.12
 6.3.2.1
 6.3.2.2
 6.3.2.3
@@ -3932,6 +3968,7 @@
 6.3.2.25
 6.3.2.26
 6.3.2.27
+6.3.2.28
 6.3.3.1
 6.3.3.2
 6.3.3.3
@@ -3970,6 +4007,7 @@
 6.4.1.4
 6.4.1.5
 6.4.1.6
+6.4.1.7
 6.5.1.1
 6.5.1.2
 6.5.1.3
diff --git a/data/rRNAstrand.nal b/data/rRNAstrand.nal
new file mode 100644
index 00000000..08913b98
--- /dev/null
+++ b/data/rRNAstrand.nal
@@ -0,0 +1,8 @@
+#
+# Alias file created 6/8/2007 by Tom Madden
+#
+#
+TITLE 16Score
+#
+DBLIST 16SCore Combined16SrRNA
+#
diff --git a/data/sequin.hlp b/data/sequin.hlp
index 805854bb..e69cde04 100644
--- a/data/sequin.hlp
+++ b/data/sequin.hlp
@@ -76,11 +76,11 @@ on the "Prev form" or "Next form" buttons on the first or last pages of
 a form, respectively.
 
 #There are numerous ways to enter information onto a page of a form,
-#including text fields, radio buttons, check boxes, scrolling boxes,
-#pop-up menus and spreadsheets.
+including text fields, radio buttons, check boxes, scrolling boxes,
+pop-up menus and spreadsheets.
 
 #You may also use tables to import annotation of source information. 
-#The formatting of these tables will be discussed below.
+The formatting of these tables will be discussed below.
 
 *Overview of Sequin
 
@@ -104,8 +104,7 @@ record, click on "Read Existing Record". If you would like to quit from
 Sequin, click on "Quit Program".
 
 #You can also "Read Existing Record" to read in a FASTA-formatted
-#sequence file
-for analysis purposes.  The sequence will be displayed in Sequin and
+sequence file for analysis purposes.  The sequence will be displayed in Sequin and
 can be analyzed with tools such as CDD Search, but it should not be
 submitted because it does not have the appropriate annotations.
 
@@ -148,7 +147,7 @@ sequences are presented in the documentation entitled
 </A> 
 and 
 <A HREF="#SequenceEditor">
-"Sequence Editor"
+Sequence Editor
 </A>
 
  respectively.  You will not see the Submitting Authors Form, the
@@ -247,7 +246,7 @@ Direct Submission.
 >Sequence Format Form
 
 #Use this form to indicate the type, format and category of sequence
-#you are submitting. 
+you are submitting. 
 
 #Sequin can process single nucleotide sequences, gapped sequences and
 sets of related sequences.  If the sequences are related in terms of
@@ -415,7 +414,11 @@ will be stripped from the sequence.  Use the IUPAC approved symbol "N"
 for ambiguous characters instead. 
 
 #A single file containing multiple FASTA sequences can be imported into
-Sequin.  Make sure that the FASTA definition line for each sequence is
+Sequin in order to create a 
+<A HREF="#SubmissionType">
+Batch Submission
+</A>
+.  Make sure that the FASTA definition line for each sequence is
 formatted as above.
 
 #If the FASTA definition line is not properly formatted a pop-up box
@@ -471,13 +474,14 @@ unknown length, the second is 234 nucleotides long.
 *FASTA+GAP Format for Aligned Nucleotide Sequences
 
 #A number of programs output sets of aligned sequences in FASTA format.
-Frequently, to align these sequences, gaps must be inserted.  Specify
-relevant gap and ambiguous characters in the appropriate box on the
-
+Frequently, to align these sequences, gaps must be inserted.  The
+default alignment settings should correctl interpret gap and ambiguous
+characters in most cases.  If Sequin can not read your alignment, you
+may need to change these settings using the Optional Alignment Settings
+button on the
 <A HREF="#NucleotidePage">
 Nucleotide Page
 </A>
-
 form.  Each sequence, including gaps, must be the same length.  The
 gaps will only show up in the alignment, not in the individual sequence
 in the database.
@@ -548,7 +552,10 @@ database, you must mark that sequence so that it does not receive a new
 Accession number.  To do this, use a SeqID in the format accU12345,
 where U12345 is the Accession number of the pre-existing sequence. 
 
-#Specify relevant gap and ambiguous characters in the appropriate box on the
+#The default alignment settings should correctly interpret gap and
+ambiguous characters in most cases.  If Sequin can not read your
+alignment, you may need to change these settings using the Optional
+Alignment Settings button on the
 <A HREF="#NucleotidePage">
 Nucleotide Page
 </A>
@@ -611,17 +618,31 @@ database, you must mark that sequence so that it does not receive a new
 Accession number.  To do this, use a SeqID in the format accU12345,
 where U12345 is the Accession number of the pre-existing sequence. 
 Also, Sequin will replace the "?" characters in the sequences with "N"s
-since they are defined as "missing" data in the header.  You should
-specify relevant gap and ambiguous characters in the appropriate box on
-the
-
+since they are defined as "missing" data in the header.  The default
+alignment settings should correctly interpret gap and ambiguous
+characters in most cases.  If Sequin can not read your alignment, you
+may need to change these settings using the Optional Alignment Settings
+button on the
 <A HREF="#NucleotidePage">
-
 Nucleotide Page
+</A>
+form.  
 
+#You can modify either NEXUS format so that Sequin can
+determine the correct organism and any other modifiers for each
+sequence.  An example of such modifications are below in the section on
+<A HREF="#SourceModifiersforPHYLIPandNEXUS">
+Source Modifiers for PHYLIP and NEXUS
 </A>
+.
+#Alternatively, you can leave your sequence alignment in
+standard NEXUS format and enter the organism, strain, chromosome, etc.
+information on the following
 
-form.
+<A HREF="#SourceModifiersForm">
+Source Modifers form
+</A>
+.
 #The following is an example of NEXUS Contiguous format.
 
 !#NEXUS
@@ -667,7 +688,7 @@ sequence.  An example of such modifications are below in the section on
 Source Modifiers for PHYLIP and NEXUS
 </A>
 .
-Alternatively, you can leave your sequence alignment in
+#Alternatively, you can leave your sequence alignment in
 standard NEXUS format and enter the organism, strain, chromosome, etc.
 information on the following
 
@@ -701,14 +722,25 @@ above.
 would follow immediately after the sequence in the PHYLIP and NEXUS
 examples, above.
 
+!;
+!END;
+!
+!begin ncbi;
+!sequin
 !>[organism=Gallus gallus] [clone=C]
 !>[organism=Drosophila melanogaster] [strain=D]
 !>[organism=Caenorhabditis elegans] [strain=E]
 !>[organism=Rattus norvegicus] [strain=F]
 !>[organism=Aspergillus nidulans] [strain=G]
+!;
+!end;
 
 #The number of lines of source information must exactly match the number
-of sequences provided.
+of sequences provided.  Complete examples can be found in the 
+<A HREF="http://www.ncbi.nlm.nih.gov/Sequin/QuickGuide/sequin.htm#AlignmentFormats">
+Alignment Formats
+</A>
+section of the Sequin Quick Guide.
 
 #Alternatively, you can leave your sequence alignment in
 standard NEXUS or PHYLIP format and enter the organism, strain, chromosome, etc.
@@ -1297,6 +1329,11 @@ you.  You do not need to fill out the 'from' and 'to' columns.  Note
 that multiple accessions may be entered to provide full coverage of the
 assembled sequence.
 
+#If the accession entered is not recognized as a GenBank Accession
+number, a pop-up box is generated requesting that you edit the numbers
+listed.  Sequences from the trace archive can be used primary sequence
+data for TPA records but must be entered in the format "TI123456789".
+
 #You may also generate an Assembly Tracking form in the record viewer
 under the Annotate menu.  Select Descriptors and TPA Assembly from the
 pull-down menu in order to generate the Assembly Tracking form.
@@ -2058,7 +2095,8 @@ strand on which the feature is found.
 #-Other:  Do not select this item.
 
 #Use the pop-up menu to select the SeqID of the sequence you are
-describing by the location.
+describing by the location.  Clicking on the X button to the left will clear
+location spans, strand, and SeqID from that row. 
 
 #If you are working on a set of sequences which contain an alignment,
 you will see a toggle at the bottom of the Location Page where you can
@@ -2165,6 +2203,19 @@ nucleotide sequence by clicking on Translate Product. However, you must
 first indicate the location and partialness of the coding region on the
 Location page in order to obtain the correct translation.
 
+#The Edit Protein Sequence button will launch an amino acid
+ <A HREF="#SequenceEditor">
+Sequence Editor
+</A>
+ as discussed below.
+
+#The Adjust for Stop Codon button will truncate a displayed translation
+at the first stop codon.   If no stop codon is present in the current
+translation, this function will extend the translation to the first stop
+codon or to the end of the sequence.  In both cases, the spans of the
+coding region will be automatically updated on the Location Page to
+reflect the new translation.
+
 ***Protein Subpage
 
 #Use this page to enter or edit a name or descriptionof the protein
@@ -2279,7 +2330,7 @@ feature key.
 #Site of any generalized, site-specific, or replicative recombination
 event where there is a breakage and reunion of duplex DNA that cannot be
 described by other recombination keys (iDNA and virion) or qualifiers of
-source key (/insertion_seq, /transposon, /proviral).
+source key (/proviral).
 
 *misc_RNA
 
@@ -2374,7 +2425,10 @@ transcription.
 
 *repeat_region
 
-#Region of genome containing repeating units.
+#Region of genome containing repeating units.  Some qualifiers such as
+rpt_type and mobile_element have controlled vocabularies.  These
+qualifiers have check boxes or pull-down menus to ensure that the
+correct format is used.
 
 *repeat_unit
 
@@ -2646,7 +2700,10 @@ and/or organism.  Entering information is optional.
 and type the appropriate name on the right side of the page.  If you do
 not find appropriate modifiers in the scroll down list, you can enter
 additional source information as text in the field at the bottom of the
-page.  You may select as many modifiers as you want.
+page.  You may add multiple modifiers to describe the source organism.
+
+#Clicking on the X button to the right of the text box will remove the
+text and clear the modifier from the pull-down in that line.
 
 #The following is a description of the available modifiers:
 
@@ -2676,8 +2733,8 @@ the chromosome of its host cell and can therefore exhibit vertical
 transmission.
 
 #-Environmental-sample: Identifies sequence derived by direct molecular
-isolation from an unidentified organism.  Do not include extra text when
-using this modifier. 
+isolation from an unidentified organism.  You cannot include extra text when
+using this modifier; the text box will change to TRUE upon selection of this modifier from the pull-down list 
 
 #-Frequency:  Frequency of occurrence of a feature.
 
@@ -2690,8 +2747,9 @@ amplification.
 
 #-Germline:  If the sequence shown is DNA and a member of the
 immunoglobulin family, this qualifier is used to denote that the sequence
-is from unrearranged DNA.  Do not include extra text when using this
-modifier. 
+is from unrearranged DNA.  You cannot include extra text when using this
+modifier; the text box will change to TRUE upon selection of this modifier
+from the pull-down list. 
 
 #-Haplotype:  Haplotype of the organism.
 
@@ -2705,10 +2763,17 @@ from which the sequence was derived
 the sequence was derived.
 
 #-Lat-Lon:  Latitude and longitude of location where sample was
-collected.  Preferred format is decimal degrees N/S E/W.
+collected.  Mandatory format is decimal degrees N/S E/W.  Selecting this
+modifier in the pull-down list will generate separate boxes for entering the
+information in the mandatory format.
 
 #-Map:  Map location of the gene.
 
+#-Metagenomic:  Identifies sequence from a culture-independent genomic
+#analysis of an environmental sample submitted as part of a whole genome
+#shotgun project.  You may not include extra text when using this modifier,
+#instead the text box will change to TRUE upon selection.
+
 #-Plasmid-name:  Name of plasmid from which the sequence was obtained.
 
 #-Plastid-name:  Name of plastid from which the sequence was obtained.
@@ -2718,13 +2783,14 @@ obtained.
 
 #-Rearranged:  If the sequence shown is DNA and a member of the
 immunoglobulin family, this qualifier is used to denote that the sequence
-is from rearranged DNA.  Do not include extra text when using this
-modifier.
+is from rearranged DNA.  You cannot include extra text when using this
+modifier; the text box will change to TRUE upon selection of this modifier
+from the pull-down list. 
 
-#Rev-PCR-primer-name:  Name or description of reverse primer used for
+#-Rev-PCR-primer-name:  Name or description of reverse primer used for
 amplification.
 
-#Rev-PCR-primer-seq:  Sequence of reverse primer used for amplification.
+#-Rev-PCR-primer-seq:  Sequence of reverse primer used for amplification.
 
 #-Segment: Name of viral genome fragmented into two or more nucleic acid
 molecules.
@@ -2737,8 +2803,9 @@ molecules.
 
 #-Tissue-type:  Type of tissue from which sequence derives.
 
-#-Transgenic:  Identified organism that was the recipient of transgenic
-DNA.  Do not include extra text when using this modifier.
+#-Transgenic:  Identifies organism was the recipient of transgenic
+DNA.  You cannot include extra text when using this modifier; the text box
+will change to TRUE upon selection of this modifier from the pull-down list. 
 
 **Organism Subpage
 
@@ -2746,7 +2813,10 @@ DNA.  Do not include extra text when using this modifier.
 and type the appropriate name on the right side of the page.  If you do
 not find appropriate modifiers in the scroll down list, you can enter
 additional organism information as text in the field at the bottom of
-the page. You may select as many modifiers as you want.
+the page. You may add multiple modifiers to describe the source organism. 
+
+#Clicking on the X button to the right of the text box will remove the text
+#and clear the modifier from the pull-down in that line.
 
 #The following is a description of the available modifiers:
 
@@ -3346,7 +3416,7 @@ from the record before submission.
 *Vector Screen
 
 #This option allows you to run a BLAST search of your nucleotide
-#sequence(s) against NCBI's 
+sequence(s) against NCBI's 
 <A HREF="http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html">
 UniVec
 </A>
@@ -3368,29 +3438,47 @@ remove this feature before submission.
 
 *ORF Finder
 
-#The ORF Finder shows a graphical representation of all the open reading
+#The ORF Finder shows a graphical representation of all open reading
 frames (ORFs) in the nucleotide sequence.  This tool allows you to
 select ORFs and have them appear as coding sequence (CDS) features on
 the sequence record. 
 
-#The ORFs, indicated by colored boxes, are defined as the longest
-sequence containing a start codon and a stop codon.  If the
-entire nucleotide sequence is an open reading frame but does not
-contain an initial start or a terminal stop codon, it will be indicated
-as an ORF as well.  All six reading frames are shown; the top three
-boxes represent the plus strands, and the bottom three boxes the minus
-strands.  The nucleotide sequence intervals of the ORFs are displayed in
-descending length order on the right side of the window.  Intervals on
-the complementary (minus) strand are indicated by a 'c'.  ORFs can be
-selected by clicking either directly on them or on the sequence
-interval.  The ORF length button selects the length of ORFs that are
+#The ORFs, indicated by colored boxes, are defined as the longest sequence
+containing a start codon and stop codon.  All six reading frames are shown as
+separate lines in the graphical view.  The top three lines represent the plus
+strands, and the bottom three lines the minus strands.  In the default view,
+the nucleotide sequence intervals of the ORFs are displayed in descending
+length order on the right side of the window.  Intervals on the complementary
+(minus) strand are indicated by a 'c'.  Selecting 'Order by Start' will
+reorder the list based on the nucleotide location of the start codon.  
+
+#Clicking on the box labelled ORF changes the graphical display so that the
+#potential start codons are indicated in white, and stop codons in red.
+
+#The default settings display only those ORFs which contain an ATG start
+codon.  Selecting 'Alternative' in the 'Initiation Codon' box, will also
+include ORFs beginning with all valid alternative start codons as determined
+by the genetic code listed in the source feature.  If the genetic code for the
+source organism has not been specified, the default
+<A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG1">
+standard genetic code 
+</A>
+will be used. 
+
+#The ORF length button sets the length of ORFs that are
 displayed.  For example, the default of 10 shows all ORFs that are
-greater than 10 nucleotides in length.  Clicking on the box labelled ORF
-changes the display; potential start codons are indicated in white, and
-stop codons in red.  ORFs can be selected in this display also.  The
-definition of start and stop codons is dependent on the genetic code
-that was selected. Be sure to choose the appropriate genetic code for
-translating the sequence before opening the ORF finder. 
+greater than 10 nucleotides in length.  
+
+#Checking the Show Partial ORFs box will display ORFs that extend to the
+#end(s) of the nucleotide sequence but are 5' or 3' partial.
+
+#ORFs can be selected by clicking on the graphical representation or on the
+sequence interval.  Once an ORF has been selected, its location and amino acid
+sequence will automatically be fielded in the
+<A HREF="#CDS">
+CDS feature editor
+</A>
+accessed under the Annotate menu. 
 
 *Select Target
 
@@ -3891,7 +3979,8 @@ side, or displayed on the top of the sequence.
 
 **Grid
 
-#Allows the display to show a grid separating each feature and sequence for easier viewing.
+#Allows the display to show a grid separating each feature and sequence for
+easier viewing.
 
 **Features Toggle
 
@@ -3995,7 +4084,7 @@ be entered as the location relative to the alignment coordinates.
 <P CLASS=medium1><B>Questions or Comments?</B>
 <BR>Write to the <A HREF="mailto:info@ncbi.nlm.nih.gov">NCBI Service
 Desk</A></P>
-<P CLASS=medium1>Revised December 2, 2005
+<P CLASS=medium1>Revised July 20, 2007
 
 </CENTER>