id	sid	tid	token	lemma	pos
cord-103204-gt6upfri	1	1	key	key	NN
cord-103204-gt6upfri	1	2	:	:	:
cord-103204-gt6upfri	2	1	cord-103204-gt6upfri	cord-103204-gt6upfri	.
cord-103204-gt6upfri	3	1	authors	author	NNS
cord-103204-gt6upfri	3	2	:	:	:
cord-103204-gt6upfri	3	3	Hölzer	Hölzer	NNP
cord-103204-gt6upfri	3	4	,	,	,
cord-103204-gt6upfri	3	5	Martin	Martin	NNP
cord-103204-gt6upfri	3	6	;	;	:
cord-103204-gt6upfri	3	7	Marz	Marz	NNP
cord-103204-gt6upfri	3	8	,	,	,
cord-103204-gt6upfri	3	9	Manja	Manja	NNP
cord-103204-gt6upfri	3	10	title	title	NN
cord-103204-gt6upfri	3	11	:	:	:
cord-103204-gt6upfri	3	12	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	3	13	:	:	:
cord-103204-gt6upfri	3	14	a	a	DT
cord-103204-gt6upfri	3	15	Nextflow	Nextflow	NNP
cord-103204-gt6upfri	3	16	pipeline	pipeline	NN
cord-103204-gt6upfri	3	17	for	for	IN
cord-103204-gt6upfri	3	18	the	the	DT
cord-103204-gt6upfri	3	19	detection	detection	NN
cord-103204-gt6upfri	3	20	of	of	IN
cord-103204-gt6upfri	3	21	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	3	22	recombination	recombination	NN
cord-103204-gt6upfri	3	23	events	event	NNS
cord-103204-gt6upfri	3	24	and	and	CC
cord-103204-gt6upfri	3	25	positive	positive	JJ
cord-103204-gt6upfri	3	26	selection	selection	NN
cord-103204-gt6upfri	3	27	date	date	NN
cord-103204-gt6upfri	3	28	:	:	:
cord-103204-gt6upfri	3	29	2020	2020	CD
cord-103204-gt6upfri	3	30	-	-	HYPH
cord-103204-gt6upfri	3	31	05	05	CD
cord-103204-gt6upfri	3	32	-	-	HYPH
cord-103204-gt6upfri	3	33	20	20	CD
cord-103204-gt6upfri	3	34	journal	journal	NN
cord-103204-gt6upfri	3	35	:	:	:
cord-103204-gt6upfri	4	1	bioRxiv	biorxiv	IN
cord-103204-gt6upfri	4	2	DOI	DOI	NNP
cord-103204-gt6upfri	4	3	:	:	:
cord-103204-gt6upfri	5	1	10.1101/2020.05.18.102731	10.1101/2020.05.18.102731	CD
cord-103204-gt6upfri	6	1	sha	sha	NNP
cord-103204-gt6upfri	6	2	:	:	:
cord-103204-gt6upfri	6	3	bce116dd6608b571784241a4b2da8e177da9c6ac	bce116dd6608b571784241a4b2da8e177da9c6ac	NNP
cord-103204-gt6upfri	6	4	doc_id	doc_id	NNP
cord-103204-gt6upfri	6	5	:	:	:
cord-103204-gt6upfri	6	6	103204	103204	CD
cord-103204-gt6upfri	6	7	cord_uid	cord_uid	NNS
cord-103204-gt6upfri	6	8	:	:	:
cord-103204-gt6upfri	7	1	gt6upfri	gt6upfri	.
cord-103204-gt6upfri	8	1	Summary	Summary	NNP
cord-103204-gt6upfri	8	2	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	8	3	is	be	VBZ
cord-103204-gt6upfri	8	4	an	an	DT
cord-103204-gt6upfri	8	5	easy	easy	JJ
cord-103204-gt6upfri	8	6	-	-	HYPH
cord-103204-gt6upfri	8	7	to	to	IN
cord-103204-gt6upfri	8	8	-	-	HYPH
cord-103204-gt6upfri	8	9	use	use	NN
cord-103204-gt6upfri	8	10	pipeline	pipeline	NN
cord-103204-gt6upfri	8	11	that	that	WDT
cord-103204-gt6upfri	8	12	helps	help	VBZ
cord-103204-gt6upfri	8	13	researchers	researcher	NNS
cord-103204-gt6upfri	8	14	to	to	TO
cord-103204-gt6upfri	8	15	find	find	VB
cord-103204-gt6upfri	8	16	recombination	recombination	NN
cord-103204-gt6upfri	8	17	events	event	NNS
cord-103204-gt6upfri	8	18	and	and	CC
cord-103204-gt6upfri	8	19	sites	site	NNS
cord-103204-gt6upfri	8	20	under	under	IN
cord-103204-gt6upfri	8	21	positive	positive	JJ
cord-103204-gt6upfri	8	22	selection	selection	NN
cord-103204-gt6upfri	8	23	in	in	IN
cord-103204-gt6upfri	8	24	protein	protein	NN
cord-103204-gt6upfri	8	25	-	-	HYPH
cord-103204-gt6upfri	8	26	coding	code	VBG
cord-103204-gt6upfri	8	27	sequences	sequence	NNS
cord-103204-gt6upfri	8	28	.	.	.
cord-103204-gt6upfri	9	1	By	by	IN
cord-103204-gt6upfri	9	2	entering	enter	VBG
cord-103204-gt6upfri	9	3	homologous	homologous	JJ
cord-103204-gt6upfri	9	4	sequences	sequence	NNS
cord-103204-gt6upfri	9	5	,	,	,
cord-103204-gt6upfri	9	6	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	9	7	builds	build	VBZ
cord-103204-gt6upfri	9	8	an	an	DT
cord-103204-gt6upfri	9	9	alignment	alignment	NN
cord-103204-gt6upfri	9	10	,	,	,
cord-103204-gt6upfri	9	11	estimates	estimate	VBZ
cord-103204-gt6upfri	9	12	a	a	DT
cord-103204-gt6upfri	9	13	best	well	RBS
cord-103204-gt6upfri	9	14	-	-	HYPH
cord-103204-gt6upfri	9	15	fitting	fitting	JJ
cord-103204-gt6upfri	9	16	substitution	substitution	NN
cord-103204-gt6upfri	9	17	model	model	NN
cord-103204-gt6upfri	9	18	,	,	,
cord-103204-gt6upfri	9	19	and	and	CC
cord-103204-gt6upfri	9	20	performs	perform	VBZ
cord-103204-gt6upfri	9	21	a	a	DT
cord-103204-gt6upfri	9	22	recombination	recombination	NN
cord-103204-gt6upfri	9	23	analysis	analysis	NN
cord-103204-gt6upfri	9	24	followed	follow	VBN
cord-103204-gt6upfri	9	25	by	by	IN
cord-103204-gt6upfri	9	26	the	the	DT
cord-103204-gt6upfri	9	27	construction	construction	NN
cord-103204-gt6upfri	9	28	of	of	IN
cord-103204-gt6upfri	9	29	all	all	DT
cord-103204-gt6upfri	9	30	corresponding	correspond	VBG
cord-103204-gt6upfri	9	31	phylogenies	phylogeny	NNS
cord-103204-gt6upfri	9	32	.	.	.
cord-103204-gt6upfri	10	1	Finally	finally	RB
cord-103204-gt6upfri	10	2	,	,	,
cord-103204-gt6upfri	10	3	significantly	significantly	RB
cord-103204-gt6upfri	10	4	positive	positive	JJ
cord-103204-gt6upfri	10	5	selected	select	VBN
cord-103204-gt6upfri	10	6	sites	site	NNS
cord-103204-gt6upfri	10	7	are	be	VBP
cord-103204-gt6upfri	10	8	detected	detect	VBN
cord-103204-gt6upfri	10	9	according	accord	VBG
cord-103204-gt6upfri	10	10	to	to	IN
cord-103204-gt6upfri	10	11	different	different	JJ
cord-103204-gt6upfri	10	12	models	model	NNS
cord-103204-gt6upfri	10	13	for	for	IN
cord-103204-gt6upfri	10	14	the	the	DT
cord-103204-gt6upfri	10	15	full	full	JJ
cord-103204-gt6upfri	10	16	alignment	alignment	NN
cord-103204-gt6upfri	10	17	and	and	CC
cord-103204-gt6upfri	10	18	possible	possible	JJ
cord-103204-gt6upfri	10	19	recombination	recombination	NN
cord-103204-gt6upfri	10	20	fragments	fragment	NNS
cord-103204-gt6upfri	10	21	.	.	.
cord-103204-gt6upfri	11	1	The	the	DT
cord-103204-gt6upfri	11	2	results	result	NNS
cord-103204-gt6upfri	11	3	of	of	IN
cord-103204-gt6upfri	11	4	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	11	5	are	be	VBP
cord-103204-gt6upfri	11	6	summarized	summarize	VBN
cord-103204-gt6upfri	11	7	in	in	IN
cord-103204-gt6upfri	11	8	a	a	DT
cord-103204-gt6upfri	11	9	user	user	NN
cord-103204-gt6upfri	11	10	-	-	HYPH
cord-103204-gt6upfri	11	11	friendly	friendly	JJ
cord-103204-gt6upfri	11	12	HTML	html	NN
cord-103204-gt6upfri	11	13	page	page	NN
cord-103204-gt6upfri	11	14	providing	provide	VBG
cord-103204-gt6upfri	11	15	all	all	DT
cord-103204-gt6upfri	11	16	intermediate	intermediate	JJ
cord-103204-gt6upfri	11	17	results	result	NNS
cord-103204-gt6upfri	11	18	and	and	CC
cord-103204-gt6upfri	11	19	the	the	DT
cord-103204-gt6upfri	11	20	graphical	graphical	JJ
cord-103204-gt6upfri	11	21	representation	representation	NN
cord-103204-gt6upfri	11	22	of	of	IN
cord-103204-gt6upfri	11	23	recombination	recombination	NN
cord-103204-gt6upfri	11	24	events	event	NNS
cord-103204-gt6upfri	11	25	and	and	CC
cord-103204-gt6upfri	11	26	positively	positively	RB
cord-103204-gt6upfri	11	27	selected	select	VBN
cord-103204-gt6upfri	11	28	sites	site	NNS
cord-103204-gt6upfri	11	29	.	.	.
cord-103204-gt6upfri	12	1	Availability	availability	NN
cord-103204-gt6upfri	12	2	and	and	CC
cord-103204-gt6upfri	12	3	implementation	implementation	NN
cord-103204-gt6upfri	12	4	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	12	5	is	be	VBZ
cord-103204-gt6upfri	12	6	freely	freely	RB
cord-103204-gt6upfri	12	7	available	available	JJ
cord-103204-gt6upfri	12	8	at	at	IN
cord-103204-gt6upfri	12	9	https://github.com/hoelzer/poseidon	https://github.com/hoelzer/poseidon	NNP
cord-103204-gt6upfri	12	10	.	.	.
cord-103204-gt6upfri	13	1	The	the	DT
cord-103204-gt6upfri	13	2	pipeline	pipeline	NN
cord-103204-gt6upfri	13	3	is	be	VBZ
cord-103204-gt6upfri	13	4	implemented	implement	VBN
cord-103204-gt6upfri	13	5	in	in	IN
cord-103204-gt6upfri	13	6	Nextflow	Nextflow	NNP
cord-103204-gt6upfri	13	7	with	with	IN
cord-103204-gt6upfri	13	8	Docker	Docker	NNP
cord-103204-gt6upfri	13	9	support	support	NN
cord-103204-gt6upfri	13	10	and	and	CC
cord-103204-gt6upfri	13	11	processes	process	VBZ
cord-103204-gt6upfri	13	12	the	the	DT
cord-103204-gt6upfri	13	13	output	output	NN
cord-103204-gt6upfri	13	14	of	of	IN
cord-103204-gt6upfri	13	15	various	various	JJ
cord-103204-gt6upfri	13	16	tools	tool	NNS
cord-103204-gt6upfri	13	17	.	.	.
cord-103204-gt6upfri	14	1	Contact	contact	NN
cord-103204-gt6upfri	14	2	hoelzer.martin@gmail.com	hoelzer.martin@gmail.com	ADD
cord-103204-gt6upfri	15	1	Selection	selection	NN
cord-103204-gt6upfri	15	2	pressure	pressure	NN
cord-103204-gt6upfri	15	3	continuously	continuously	RB
cord-103204-gt6upfri	15	4	influences	influence	VBZ
cord-103204-gt6upfri	15	5	the	the	DT
cord-103204-gt6upfri	15	6	evolution	evolution	NN
cord-103204-gt6upfri	15	7	of	of	IN
cord-103204-gt6upfri	15	8	genes	gene	NNS
cord-103204-gt6upfri	15	9	and	and	CC
cord-103204-gt6upfri	15	10	can	can	MD
cord-103204-gt6upfri	15	11	be	be	VB
cord-103204-gt6upfri	15	12	studied	study	VBN
cord-103204-gt6upfri	15	13	in	in	IN
cord-103204-gt6upfri	15	14	many	many	JJ
cord-103204-gt6upfri	15	15	ways	way	NNS
cord-103204-gt6upfri	15	16	(	(	-LRB-
cord-103204-gt6upfri	15	17	Vitti	Vitti	NNP
cord-103204-gt6upfri	15	18	et	et	NNP
cord-103204-gt6upfri	15	19	al	al	NNP
cord-103204-gt6upfri	15	20	.	.	NNP
cord-103204-gt6upfri	15	21	,	,	,
cord-103204-gt6upfri	15	22	2013	2013	CD
cord-103204-gt6upfri	15	23	)	)	-RRB-
cord-103204-gt6upfri	15	24	.	.	.
cord-103204-gt6upfri	16	1	For	for	IN
cord-103204-gt6upfri	16	2	example	example	NN
cord-103204-gt6upfri	16	3	,	,	,
cord-103204-gt6upfri	16	4	positive	positive	JJ
cord-103204-gt6upfri	16	5	or	or	CC
cord-103204-gt6upfri	16	6	diversifying	diversify	VBG
cord-103204-gt6upfri	16	7	selection	selection	NN
cord-103204-gt6upfri	16	8	can	can	MD
cord-103204-gt6upfri	16	9	be	be	VB
cord-103204-gt6upfri	16	10	detected	detect	VBN
cord-103204-gt6upfri	16	11	by	by	IN
cord-103204-gt6upfri	16	12	comparing	compare	VBG
cord-103204-gt6upfri	16	13	the	the	DT
cord-103204-gt6upfri	16	14	rates	rate	NNS
cord-103204-gt6upfri	16	15	of	of	IN
cord-103204-gt6upfri	16	16	non	non	JJ
cord-103204-gt6upfri	16	17	-	-	JJ
cord-103204-gt6upfri	16	18	synonymous	synonymous	JJ
cord-103204-gt6upfri	16	19	(	(	-LRB-
cord-103204-gt6upfri	16	20	dN	dn	NN
cord-103204-gt6upfri	16	21	)	)	-RRB-
cord-103204-gt6upfri	16	22	and	and	CC
cord-103204-gt6upfri	16	23	synonymous	synonymous	JJ
cord-103204-gt6upfri	16	24	substitutions	substitution	NNS
cord-103204-gt6upfri	16	25	(	(	-LRB-
cord-103204-gt6upfri	16	26	dS	dS	NNP
cord-103204-gt6upfri	16	27	)	)	-RRB-
cord-103204-gt6upfri	16	28	in	in	IN
cord-103204-gt6upfri	16	29	an	an	DT
cord-103204-gt6upfri	16	30	alignment	alignment	NN
cord-103204-gt6upfri	16	31	of	of	IN
cord-103204-gt6upfri	16	32	orthologous	orthologous	JJ
cord-103204-gt6upfri	16	33	genes	gene	NNS
cord-103204-gt6upfri	16	34	.	.	.
cord-103204-gt6upfri	17	1	Over	over	IN
cord-103204-gt6upfri	17	2	several	several	JJ
cord-103204-gt6upfri	17	3	sites	site	NNS
cord-103204-gt6upfri	17	4	(	(	-LRB-
cord-103204-gt6upfri	17	5	codons	codon	NNS
cord-103204-gt6upfri	17	6	)	)	-RRB-
cord-103204-gt6upfri	17	7	,	,	,
cord-103204-gt6upfri	17	8	the	the	DT
cord-103204-gt6upfri	17	9	dN	dN	NNP
cord-103204-gt6upfri	17	10	/	/	SYM
cord-103204-gt6upfri	17	11	dS	ds	NN
cord-103204-gt6upfri	17	12	ratio	ratio	NN
cord-103204-gt6upfri	17	13	(	(	-LRB-
cord-103204-gt6upfri	17	14	or	or	CC
cord-103204-gt6upfri	17	15	ω	ω	LS
cord-103204-gt6upfri	17	16	)	)	-RRB-
cord-103204-gt6upfri	17	17	can	can	MD
cord-103204-gt6upfri	17	18	reach	reach	VB
cord-103204-gt6upfri	17	19	values	value	NNS
cord-103204-gt6upfri	17	20	well	well	RB
cord-103204-gt6upfri	17	21	above	above	IN
cord-103204-gt6upfri	17	22	1	1	CD
cord-103204-gt6upfri	17	23	(	(	-LRB-
cord-103204-gt6upfri	17	24	Yang	Yang	NNP
cord-103204-gt6upfri	17	25	,	,	,
cord-103204-gt6upfri	17	26	2007	2007	CD
cord-103204-gt6upfri	17	27	)	)	-RRB-
cord-103204-gt6upfri	17	28	,	,	,
cord-103204-gt6upfri	17	29	and	and	CC
cord-103204-gt6upfri	17	30	such	such	JJ
cord-103204-gt6upfri	17	31	sites	site	NNS
cord-103204-gt6upfri	17	32	are	be	VBP
cord-103204-gt6upfri	17	33	likely	likely	JJ
cord-103204-gt6upfri	17	34	to	to	TO
cord-103204-gt6upfri	17	35	be	be	VB
cord-103204-gt6upfri	17	36	positively	positively	RB
cord-103204-gt6upfri	17	37	selected	select	VBN
cord-103204-gt6upfri	17	38	.	.	.
cord-103204-gt6upfri	18	1	For	for	IN
cord-103204-gt6upfri	18	2	instance	instance	NN
cord-103204-gt6upfri	18	3	,	,	,
cord-103204-gt6upfri	18	4	specific	specific	JJ
cord-103204-gt6upfri	18	5	amino	amino	NN
cord-103204-gt6upfri	18	6	acid	acid	NN
cord-103204-gt6upfri	18	7	changes	change	NNS
cord-103204-gt6upfri	18	8	are	be	VBP
cord-103204-gt6upfri	18	9	favored	favor	VBN
cord-103204-gt6upfri	18	10	if	if	IN
cord-103204-gt6upfri	18	11	they	-PRON-	PRP
cord-103204-gt6upfri	18	12	increase	increase	VBP
cord-103204-gt6upfri	18	13	the	the	DT
cord-103204-gt6upfri	18	14	host	host	NN
cord-103204-gt6upfri	18	15	's	's	POS
cord-103204-gt6upfri	18	16	fitness	fitness	NN
cord-103204-gt6upfri	18	17	against	against	IN
cord-103204-gt6upfri	18	18	a	a	DT
cord-103204-gt6upfri	18	19	pathogen	pathogen	NN
cord-103204-gt6upfri	18	20	(	(	-LRB-
cord-103204-gt6upfri	18	21	Fumagalli	Fumagalli	NNP
cord-103204-gt6upfri	18	22	et	et	FW
cord-103204-gt6upfri	18	23	al	al	NNP
cord-103204-gt6upfri	18	24	.	.	NNP
cord-103204-gt6upfri	18	25	,	,	,
cord-103204-gt6upfri	18	26	2011	2011	CD
cord-103204-gt6upfri	18	27	)	)	-RRB-
cord-103204-gt6upfri	18	28	.	.	.
cord-103204-gt6upfri	19	1	Alternatively	alternatively	RB
cord-103204-gt6upfri	19	2	,	,	,
cord-103204-gt6upfri	19	3	the	the	DT
cord-103204-gt6upfri	19	4	genes	gene	NNS
cord-103204-gt6upfri	19	5	of	of	IN
cord-103204-gt6upfri	19	6	a	a	DT
cord-103204-gt6upfri	19	7	pathogen	pathogen	NN
cord-103204-gt6upfri	19	8	are	be	VBP
cord-103204-gt6upfri	19	9	affected	affect	VBN
cord-103204-gt6upfri	19	10	,	,	,
cord-103204-gt6upfri	19	11	as	as	IN
cord-103204-gt6upfri	19	12	in	in	IN
cord-103204-gt6upfri	19	13	the	the	DT
cord-103204-gt6upfri	19	14	COVID	COVID	NNP
cord-103204-gt6upfri	19	15	19	19	CD
cord-103204-gt6upfri	19	16	pandemic	pandemic	NN
cord-103204-gt6upfri	19	17	,	,	,
cord-103204-gt6upfri	19	18	where	where	WRB
cord-103204-gt6upfri	19	19	positively	positively	RB
cord-103204-gt6upfri	19	20	selected	select	VBN
cord-103204-gt6upfri	19	21	sites	site	NNS
cord-103204-gt6upfri	19	22	in	in	IN
cord-103204-gt6upfri	19	23	the	the	DT
cord-103204-gt6upfri	19	24	spike	spike	NN
cord-103204-gt6upfri	19	25	protein	protein	NN
cord-103204-gt6upfri	19	26	of	of	IN
cord-103204-gt6upfri	19	27	the	the	DT
cord-103204-gt6upfri	19	28	virus	virus	NN
cord-103204-gt6upfri	19	29	gave	give	VBD
cord-103204-gt6upfri	19	30	cause	cause	NN
cord-103204-gt6upfri	19	31	for	for	IN
cord-103204-gt6upfri	19	32	concern	concern	NN
cord-103204-gt6upfri	20	1	(	(	-LRB-
cord-103204-gt6upfri	20	2	Korber	Korber	NNP
cord-103204-gt6upfri	20	3	et	et	NNP
cord-103204-gt6upfri	20	4	al	al	NNP
cord-103204-gt6upfri	20	5	.	.	NNP
cord-103204-gt6upfri	20	6	,	,	,
cord-103204-gt6upfri	20	7	2020	2020	CD
cord-103204-gt6upfri	20	8	)	)	-RRB-
cord-103204-gt6upfri	20	9	.	.	.
cord-103204-gt6upfri	21	1	The	the	DT
cord-103204-gt6upfri	21	2	detection	detection	NN
cord-103204-gt6upfri	21	3	of	of	IN
cord-103204-gt6upfri	21	4	positive	positive	JJ
cord-103204-gt6upfri	21	5	selection	selection	NN
cord-103204-gt6upfri	21	6	enables	enable	VBZ
cord-103204-gt6upfri	21	7	researchers	researcher	NNS
cord-103204-gt6upfri	21	8	to	to	TO
cord-103204-gt6upfri	21	9	gain	gain	VB
cord-103204-gt6upfri	21	10	insights	insight	NNS
cord-103204-gt6upfri	21	11	into	into	IN
cord-103204-gt6upfri	21	12	the	the	DT
cord-103204-gt6upfri	21	13	evolution	evolution	NN
cord-103204-gt6upfri	21	14	of	of	IN
cord-103204-gt6upfri	21	15	genes	gene	NNS
cord-103204-gt6upfri	21	16	and	and	CC
cord-103204-gt6upfri	21	17	thus	thus	RB
cord-103204-gt6upfri	21	18	develop	develop	VB
cord-103204-gt6upfri	21	19	countermeasures	countermeasure	NNS
cord-103204-gt6upfri	21	20	against	against	IN
cord-103204-gt6upfri	21	21	pathogens	pathogen	NNS
cord-103204-gt6upfri	21	22	that	that	WDT
cord-103204-gt6upfri	21	23	are	be	VBP
cord-103204-gt6upfri	21	24	in	in	IN
cord-103204-gt6upfri	21	25	a	a	DT
cord-103204-gt6upfri	21	26	constant	constant	JJ
cord-103204-gt6upfri	21	27	'	'	``
cord-103204-gt6upfri	21	28	arms	arm	NNS
cord-103204-gt6upfri	21	29	-	-	HYPH
cord-103204-gt6upfri	21	30	race	race	NN
cord-103204-gt6upfri	21	31	'	'	''
cord-103204-gt6upfri	21	32	with	with	IN
cord-103204-gt6upfri	21	33	their	-PRON-	PRP$
cord-103204-gt6upfri	21	34	host	host	NN
cord-103204-gt6upfri	21	35	.	.	.
cord-103204-gt6upfri	22	1	Since	since	IN
cord-103204-gt6upfri	22	2	recombination	recombination	NN
cord-103204-gt6upfri	22	3	can	can	MD
cord-103204-gt6upfri	22	4	have	have	VB
cord-103204-gt6upfri	22	5	a	a	DT
cord-103204-gt6upfri	22	6	profound	profound	JJ
cord-103204-gt6upfri	22	7	influence	influence	NN
cord-103204-gt6upfri	22	8	on	on	IN
cord-103204-gt6upfri	22	9	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	22	10	processes	process	NNS
cord-103204-gt6upfri	22	11	and	and	CC
cord-103204-gt6upfri	22	12	can	can	MD
cord-103204-gt6upfri	22	13	adversely	adversely	RB
cord-103204-gt6upfri	22	14	affect	affect	VB
cord-103204-gt6upfri	22	15	phylogenetic	phylogenetic	JJ
cord-103204-gt6upfri	22	16	reconstruction	reconstruction	NN
cord-103204-gt6upfri	22	17	and	and	CC
cord-103204-gt6upfri	22	18	the	the	DT
cord-103204-gt6upfri	22	19	accurate	accurate	JJ
cord-103204-gt6upfri	22	20	detection	detection	NN
cord-103204-gt6upfri	22	21	of	of	IN
cord-103204-gt6upfri	22	22	positive	positive	JJ
cord-103204-gt6upfri	22	23	selection	selection	NN
cord-103204-gt6upfri	22	24	(	(	-LRB-
cord-103204-gt6upfri	22	25	Shriner	Shriner	NNP
cord-103204-gt6upfri	22	26	et	et	NNP
cord-103204-gt6upfri	22	27	al	al	NNP
cord-103204-gt6upfri	22	28	.	.	NNP
cord-103204-gt6upfri	22	29	,	,	,
cord-103204-gt6upfri	22	30	2003	2003	CD
cord-103204-gt6upfri	22	31	)	)	-RRB-
cord-103204-gt6upfri	22	32	,	,	,
cord-103204-gt6upfri	22	33	screening	screen	VBG
cord-103204-gt6upfri	22	34	for	for	IN
cord-103204-gt6upfri	22	35	breakpoints	breakpoint	NNS
cord-103204-gt6upfri	22	36	to	to	TO
cord-103204-gt6upfri	22	37	define	define	VB
cord-103204-gt6upfri	22	38	recombinant	recombinant	JJ
cord-103204-gt6upfri	22	39	parts	part	NNS
cord-103204-gt6upfri	22	40	within	within	IN
cord-103204-gt6upfri	22	41	an	an	DT
cord-103204-gt6upfri	22	42	alignment	alignment	NN
cord-103204-gt6upfri	22	43	should	should	MD
cord-103204-gt6upfri	22	44	be	be	VB
cord-103204-gt6upfri	22	45	a	a	DT
cord-103204-gt6upfri	22	46	standard	standard	JJ
cord-103204-gt6upfri	22	47	step	step	NN
cord-103204-gt6upfri	22	48	in	in	IN
cord-103204-gt6upfri	22	49	any	any	DT
cord-103204-gt6upfri	22	50	comparative	comparative	JJ
cord-103204-gt6upfri	22	51	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	22	52	study	study	NN
cord-103204-gt6upfri	22	53	.	.	.
cord-103204-gt6upfri	23	1	A	a	DT
cord-103204-gt6upfri	23	2	comprehensive	comprehensive	JJ
cord-103204-gt6upfri	23	3	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	23	4	analysis	analysis	NN
cord-103204-gt6upfri	23	5	of	of	IN
cord-103204-gt6upfri	23	6	significantly	significantly	RB
cord-103204-gt6upfri	23	7	positively	positively	RB
cord-103204-gt6upfri	23	8	selected	select	VBN
cord-103204-gt6upfri	23	9	sites	site	NNS
cord-103204-gt6upfri	23	10	consist	consist	VBP
cord-103204-gt6upfri	23	11	of	of	IN
cord-103204-gt6upfri	23	12	several	several	JJ
cord-103204-gt6upfri	23	13	complicated	complicated	JJ
cord-103204-gt6upfri	23	14	steps	step	NNS
cord-103204-gt6upfri	23	15	,	,	,
cord-103204-gt6upfri	23	16	including	include	VBG
cord-103204-gt6upfri	23	17	(	(	-LRB-
cord-103204-gt6upfri	23	18	1	1	CD
cord-103204-gt6upfri	23	19	)	)	-RRB-
cord-103204-gt6upfri	23	20	in	in	IN
cord-103204-gt6upfri	23	21	-	-	HYPH
cord-103204-gt6upfri	23	22	frame	frame	NN
cord-103204-gt6upfri	23	23	alignment	alignment	NN
cord-103204-gt6upfri	23	24	;	;	,
cord-103204-gt6upfri	23	25	(	(	-LRB-
cord-103204-gt6upfri	23	26	2	2	LS
cord-103204-gt6upfri	23	27	)	)	-RRB-
cord-103204-gt6upfri	23	28	Indel	Indel	NNP
cord-103204-gt6upfri	23	29	correction	correction	NN
cord-103204-gt6upfri	23	30	;	;	,
cord-103204-gt6upfri	23	31	(	(	-LRB-
cord-103204-gt6upfri	23	32	3	3	LS
cord-103204-gt6upfri	23	33	)	)	-RRB-
cord-103204-gt6upfri	23	34	phylogenetic	phylogenetic	JJ
cord-103204-gt6upfri	23	35	tree	tree	NN
cord-103204-gt6upfri	23	36	calculation	calculation	NN
cord-103204-gt6upfri	23	37	;	;	:
cord-103204-gt6upfri	23	38	(	(	-LRB-
cord-103204-gt6upfri	23	39	4	4	LS
cord-103204-gt6upfri	23	40	)	)	-RRB-
cord-103204-gt6upfri	23	41	selection	selection	NN
cord-103204-gt6upfri	23	42	of	of	IN
cord-103204-gt6upfri	23	43	a	a	DT
cord-103204-gt6upfri	23	44	best	well	RBS
cord-103204-gt6upfri	23	45	-	-	HYPH
cord-103204-gt6upfri	23	46	fitting	fitting	JJ
cord-103204-gt6upfri	23	47	nucleotide	nucleotide	JJ
cord-103204-gt6upfri	23	48	substitution	substitution	NN
cord-103204-gt6upfri	23	49	*	*	NFP
cord-103204-gt6upfri	23	50	To	to	TO
cord-103204-gt6upfri	23	51	whom	whom	WP
cord-103204-gt6upfri	23	52	correspondence	correspondence	NN
cord-103204-gt6upfri	23	53	should	should	MD
cord-103204-gt6upfri	23	54	be	be	VB
cord-103204-gt6upfri	23	55	addressed	address	VBN
cord-103204-gt6upfri	23	56	.	.	.
cord-103204-gt6upfri	24	1	model	model	NN
cord-103204-gt6upfri	24	2	;	;	,
cord-103204-gt6upfri	24	3	(	(	-LRB-
cord-103204-gt6upfri	24	4	5	5	LS
cord-103204-gt6upfri	24	5	)	)	-RRB-
cord-103204-gt6upfri	24	6	detection	detection	NN
cord-103204-gt6upfri	24	7	of	of	IN
cord-103204-gt6upfri	24	8	topological	topological	JJ
cord-103204-gt6upfri	24	9	incongruence	incongruence	NN
cord-103204-gt6upfri	24	10	and	and	CC
cord-103204-gt6upfri	24	11	breakpoint	breakpoint	NN
cord-103204-gt6upfri	24	12	selection	selection	NN
cord-103204-gt6upfri	24	13	to	to	TO
cord-103204-gt6upfri	24	14	describe	describe	VB
cord-103204-gt6upfri	24	15	putative	putative	JJ
cord-103204-gt6upfri	24	16	recombination	recombination	NN
cord-103204-gt6upfri	24	17	events	event	NNS
cord-103204-gt6upfri	24	18	;	;	,
cord-103204-gt6upfri	24	19	(	(	-LRB-
cord-103204-gt6upfri	24	20	6	6	LS
cord-103204-gt6upfri	24	21	)	)	-RRB-
cord-103204-gt6upfri	24	22	calculation	calculation	NN
cord-103204-gt6upfri	24	23	of	of	IN
cord-103204-gt6upfri	24	24	positively	positively	RB
cord-103204-gt6upfri	24	25	selected	select	VBN
cord-103204-gt6upfri	24	26	sites	site	NNS
cord-103204-gt6upfri	24	27	(	(	-LRB-
cord-103204-gt6upfri	24	28	ω	ω	NN
cord-103204-gt6upfri	24	29	>	>	XX
cord-103204-gt6upfri	24	30	1	1	CD
cord-103204-gt6upfri	24	31	)	)	-RRB-
cord-103204-gt6upfri	24	32	under	under	IN
cord-103204-gt6upfri	24	33	varying	vary	VBG
cord-103204-gt6upfri	24	34	models	model	NNS
cord-103204-gt6upfri	24	35	;	;	,
cord-103204-gt6upfri	24	36	(	(	-LRB-
cord-103204-gt6upfri	24	37	7	7	CD
cord-103204-gt6upfri	24	38	)	)	-RRB-
cord-103204-gt6upfri	24	39	and	and	CC
cord-103204-gt6upfri	24	40	their	-PRON-	PRP$
cord-103204-gt6upfri	24	41	impact	impact	NN
cord-103204-gt6upfri	24	42	on	on	IN
cord-103204-gt6upfri	24	43	the	the	DT
cord-103204-gt6upfri	24	44	selective	selective	JJ
cord-103204-gt6upfri	24	45	pressure	pressure	NN
cord-103204-gt6upfri	24	46	acting	act	VBG
cord-103204-gt6upfri	24	47	on	on	IN
cord-103204-gt6upfri	24	48	the	the	DT
cord-103204-gt6upfri	24	49	whole	whole	JJ
cord-103204-gt6upfri	24	50	alignment	alignment	NN
cord-103204-gt6upfri	24	51	.	.	.
cord-103204-gt6upfri	25	1	Thus	thus	RB
cord-103204-gt6upfri	25	2	,	,	,
cord-103204-gt6upfri	25	3	such	such	PDT
cord-103204-gt6upfri	25	4	an	an	DT
cord-103204-gt6upfri	25	5	analysis	analysis	NN
cord-103204-gt6upfri	25	6	involves	involve	VBZ
cord-103204-gt6upfri	25	7	dozens	dozen	NNS
cord-103204-gt6upfri	25	8	of	of	IN
cord-103204-gt6upfri	25	9	different	different	JJ
cord-103204-gt6upfri	25	10	tools	tool	NNS
cord-103204-gt6upfri	25	11	and	and	CC
cord-103204-gt6upfri	25	12	parameter	parameter	NN
cord-103204-gt6upfri	25	13	settings	setting	NNS
cord-103204-gt6upfri	25	14	.	.	.
cord-103204-gt6upfri	26	1	In	in	IN
cord-103204-gt6upfri	26	2	addition	addition	NN
cord-103204-gt6upfri	26	3	,	,	,
cord-103204-gt6upfri	26	4	the	the	DT
cord-103204-gt6upfri	26	5	results	result	NNS
cord-103204-gt6upfri	26	6	of	of	IN
cord-103204-gt6upfri	26	7	many	many	JJ
cord-103204-gt6upfri	26	8	well	well	RB
cord-103204-gt6upfri	26	9	-	-	HYPH
cord-103204-gt6upfri	26	10	established	establish	VBN
cord-103204-gt6upfri	26	11	and	and	CC
cord-103204-gt6upfri	26	12	widely	widely	RB
cord-103204-gt6upfri	26	13	used	use	VBN
cord-103204-gt6upfri	26	14	tools	tool	NNS
cord-103204-gt6upfri	26	15	in	in	IN
cord-103204-gt6upfri	26	16	this	this	DT
cord-103204-gt6upfri	26	17	field	field	NN
cord-103204-gt6upfri	26	18	of	of	IN
cord-103204-gt6upfri	26	19	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	26	20	science	science	NN
cord-103204-gt6upfri	26	21	are	be	VBP
cord-103204-gt6upfri	26	22	not	not	RB
cord-103204-gt6upfri	26	23	easy	easy	JJ
cord-103204-gt6upfri	26	24	to	to	TO
cord-103204-gt6upfri	26	25	interpret	interpret	VB
cord-103204-gt6upfri	26	26	and	and	CC
cord-103204-gt6upfri	26	27	process	process	VB
cord-103204-gt6upfri	26	28	.	.	.
cord-103204-gt6upfri	27	1	Especially	especially	RB
cord-103204-gt6upfri	27	2	,	,	,
cord-103204-gt6upfri	27	3	the	the	DT
cord-103204-gt6upfri	27	4	accurate	accurate	JJ
cord-103204-gt6upfri	27	5	detection	detection	NN
cord-103204-gt6upfri	27	6	and	and	CC
cord-103204-gt6upfri	27	7	handling	handling	NN
cord-103204-gt6upfri	27	8	of	of	IN
cord-103204-gt6upfri	27	9	putative	putative	JJ
cord-103204-gt6upfri	27	10	recombination	recombination	NN
cord-103204-gt6upfri	27	11	events	event	NNS
cord-103204-gt6upfri	27	12	is	be	VBZ
cord-103204-gt6upfri	27	13	a	a	DT
cord-103204-gt6upfri	27	14	challenging	challenging	JJ
cord-103204-gt6upfri	27	15	but	but	CC
cord-103204-gt6upfri	27	16	essential	essential	JJ
cord-103204-gt6upfri	27	17	task	task	NN
cord-103204-gt6upfri	27	18	.	.	.
cord-103204-gt6upfri	28	1	Currently	currently	RB
cord-103204-gt6upfri	28	2	,	,	,
cord-103204-gt6upfri	28	3	only	only	RB
cord-103204-gt6upfri	28	4	a	a	DT
cord-103204-gt6upfri	28	5	few	few	JJ
cord-103204-gt6upfri	28	6	tools	tool	NNS
cord-103204-gt6upfri	28	7	for	for	IN
cord-103204-gt6upfri	28	8	the	the	DT
cord-103204-gt6upfri	28	9	comprehensive	comprehensive	JJ
cord-103204-gt6upfri	28	10	detection	detection	NN
cord-103204-gt6upfri	28	11	of	of	IN
cord-103204-gt6upfri	28	12	positive	positive	JJ
cord-103204-gt6upfri	28	13	selection	selection	NN
cord-103204-gt6upfri	28	14	exist	exist	VBP
cord-103204-gt6upfri	28	15	.	.	.
cord-103204-gt6upfri	29	1	These	these	DT
cord-103204-gt6upfri	29	2	tools	tool	NNS
cord-103204-gt6upfri	29	3	either	either	CC
cord-103204-gt6upfri	29	4	do	do	VBP
cord-103204-gt6upfri	29	5	not	not	RB
cord-103204-gt6upfri	29	6	automatically	automatically	RB
cord-103204-gt6upfri	29	7	combine	combine	VB
cord-103204-gt6upfri	29	8	all	all	DT
cord-103204-gt6upfri	29	9	of	of	IN
cord-103204-gt6upfri	29	10	the	the	DT
cord-103204-gt6upfri	29	11	described	describe	VBN
cord-103204-gt6upfri	29	12	steps	step	NNS
cord-103204-gt6upfri	29	13	(	(	-LRB-
cord-103204-gt6upfri	29	14	Delport	Delport	NNP
cord-103204-gt6upfri	29	15	et	et	NNP
cord-103204-gt6upfri	29	16	al	al	NNP
cord-103204-gt6upfri	29	17	.	.	NNP
cord-103204-gt6upfri	29	18	,	,	,
cord-103204-gt6upfri	29	19	2010	2010	CD
cord-103204-gt6upfri	29	20	)	)	-RRB-
cord-103204-gt6upfri	29	21	,	,	,
cord-103204-gt6upfri	29	22	do	do	VBP
cord-103204-gt6upfri	29	23	not	not	RB
cord-103204-gt6upfri	29	24	take	take	VB
cord-103204-gt6upfri	29	25	possible	possible	JJ
cord-103204-gt6upfri	29	26	recombination	recombination	NN
cord-103204-gt6upfri	29	27	events	event	NNS
cord-103204-gt6upfri	29	28	into	into	IN
cord-103204-gt6upfri	29	29	account	account	NN
cord-103204-gt6upfri	30	1	(	(	-LRB-
cord-103204-gt6upfri	30	2	Doron	Doron	NNP
cord-103204-gt6upfri	30	3	-	-	HYPH
cord-103204-gt6upfri	30	4	Faigenboim	Faigenboim	NNP
cord-103204-gt6upfri	30	5	et	et	NNP
cord-103204-gt6upfri	30	6	al	al	NNP
cord-103204-gt6upfri	30	7	.	.	.
cord-103204-gt6upfri	31	1	,	,	,
cord-103204-gt6upfri	31	2	2005	2005	CD
cord-103204-gt6upfri	31	3	;	;	:
cord-103204-gt6upfri	31	4	Stern	Stern	NNP
cord-103204-gt6upfri	31	5	et	et	FW
cord-103204-gt6upfri	31	6	al	al	NNP
cord-103204-gt6upfri	31	7	.	.	NNP
cord-103204-gt6upfri	31	8	,	,	,
cord-103204-gt6upfri	31	9	2007	2007	CD
cord-103204-gt6upfri	31	10	;	;	:
cord-103204-gt6upfri	31	11	Webb	Webb	NNP
cord-103204-gt6upfri	31	12	et	et	NNP
cord-103204-gt6upfri	31	13	al	al	NNP
cord-103204-gt6upfri	31	14	.	.	NNP
cord-103204-gt6upfri	31	15	,	,	,
cord-103204-gt6upfri	31	16	2017	2017	CD
cord-103204-gt6upfri	31	17	)	)	-RRB-
cord-103204-gt6upfri	31	18	,	,	,
cord-103204-gt6upfri	31	19	or	or	CC
cord-103204-gt6upfri	31	20	focus	focus	VBP
cord-103204-gt6upfri	31	21	only	only	RB
cord-103204-gt6upfri	31	22	on	on	IN
cord-103204-gt6upfri	31	23	the	the	DT
cord-103204-gt6upfri	31	24	detection	detection	NN
cord-103204-gt6upfri	31	25	of	of	IN
cord-103204-gt6upfri	31	26	positive	positive	JJ
cord-103204-gt6upfri	31	27	selection	selection	NN
cord-103204-gt6upfri	31	28	in	in	IN
cord-103204-gt6upfri	31	29	prokaryotic	prokaryotic	JJ
cord-103204-gt6upfri	31	30	genomes	genome	NNS
cord-103204-gt6upfri	31	31	(	(	-LRB-
cord-103204-gt6upfri	31	32	Su	Su	NNP
cord-103204-gt6upfri	31	33	et	et	FW
cord-103204-gt6upfri	31	34	al	al	NNP
cord-103204-gt6upfri	31	35	.	.	NNP
cord-103204-gt6upfri	31	36	,	,	,
cord-103204-gt6upfri	31	37	2013	2013	CD
cord-103204-gt6upfri	31	38	)	)	-RRB-
cord-103204-gt6upfri	31	39	.	.	.
cord-103204-gt6upfri	32	1	Here	here	RB
cord-103204-gt6upfri	32	2	we	-PRON-	PRP
cord-103204-gt6upfri	32	3	present	present	VBP
cord-103204-gt6upfri	32	4	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	32	5	,	,	,
cord-103204-gt6upfri	32	6	a	a	DT
cord-103204-gt6upfri	32	7	pipeline	pipeline	NN
cord-103204-gt6upfri	32	8	that	that	WDT
cord-103204-gt6upfri	32	9	allows	allow	VBZ
cord-103204-gt6upfri	32	10	researchers	researcher	NNS
cord-103204-gt6upfri	32	11	to	to	TO
cord-103204-gt6upfri	32	12	perform	perform	VB
cord-103204-gt6upfri	32	13	comprehensive	comprehensive	JJ
cord-103204-gt6upfri	32	14	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	32	15	studies	study	NNS
cord-103204-gt6upfri	32	16	by	by	IN
cord-103204-gt6upfri	32	17	automatically	automatically	RB
cord-103204-gt6upfri	32	18	taking	take	VBG
cord-103204-gt6upfri	32	19	care	care	NN
cord-103204-gt6upfri	32	20	of	of	IN
cord-103204-gt6upfri	32	21	all	all	DT
cord-103204-gt6upfri	32	22	tasks	task	NNS
cord-103204-gt6upfri	32	23	mentioned	mention	VBN
cord-103204-gt6upfri	32	24	above	above	RB
cord-103204-gt6upfri	32	25	.	.	.
cord-103204-gt6upfri	33	1	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	33	2	does	do	VBZ
cord-103204-gt6upfri	33	3	detect	detect	VB
cord-103204-gt6upfri	33	4	not	not	RB
cord-103204-gt6upfri	33	5	only	only	RB
cord-103204-gt6upfri	33	6	positively	positively	RB
cord-103204-gt6upfri	33	7	selected	select	VBN
cord-103204-gt6upfri	33	8	sites	site	NNS
cord-103204-gt6upfri	33	9	in	in	IN
cord-103204-gt6upfri	33	10	an	an	DT
cord-103204-gt6upfri	33	11	alignment	alignment	NN
cord-103204-gt6upfri	33	12	of	of	IN
cord-103204-gt6upfri	33	13	homologous	homologous	JJ
cord-103204-gt6upfri	33	14	sequences	sequence	NNS
cord-103204-gt6upfri	33	15	but	but	CC
cord-103204-gt6upfri	33	16	also	also	RB
cord-103204-gt6upfri	33	17	possible	possible	JJ
cord-103204-gt6upfri	33	18	recombination	recombination	NN
cord-103204-gt6upfri	33	19	events	event	NNS
cord-103204-gt6upfri	33	20	that	that	WDT
cord-103204-gt6upfri	33	21	could	could	MD
cord-103204-gt6upfri	33	22	otherwise	otherwise	RB
cord-103204-gt6upfri	33	23	adversely	adversely	RB
cord-103204-gt6upfri	33	24	affect	affect	VB
cord-103204-gt6upfri	33	25	the	the	DT
cord-103204-gt6upfri	33	26	positive	positive	JJ
cord-103204-gt6upfri	33	27	selection	selection	NN
cord-103204-gt6upfri	33	28	detection	detection	NN
cord-103204-gt6upfri	33	29	.	.	.
cord-103204-gt6upfri	34	1	The	the	DT
cord-103204-gt6upfri	34	2	input	input	NN
cord-103204-gt6upfri	34	3	is	be	VBZ
cord-103204-gt6upfri	34	4	a	a	DT
cord-103204-gt6upfri	34	5	single	single	JJ
cord-103204-gt6upfri	34	6	FASTA	FASTA	NNP
cord-103204-gt6upfri	34	7	file	file	NN
cord-103204-gt6upfri	34	8	consisting	consist	VBG
cord-103204-gt6upfri	34	9	of	of	IN
cord-103204-gt6upfri	34	10	protein	protein	NN
cord-103204-gt6upfri	34	11	-	-	HYPH
cord-103204-gt6upfri	34	12	coding	code	VBG
cord-103204-gt6upfri	34	13	DNA	dna	NN
cord-103204-gt6upfri	34	14	sequences	sequence	NNS
cord-103204-gt6upfri	34	15	with	with	IN
cord-103204-gt6upfri	34	16	a	a	DT
cord-103204-gt6upfri	34	17	correct	correct	JJ
cord-103204-gt6upfri	34	18	open	open	JJ
cord-103204-gt6upfri	34	19	reading	reading	NN
cord-103204-gt6upfri	34	20	frame	frame	NN
cord-103204-gt6upfri	34	21	.	.	.
cord-103204-gt6upfri	35	1	The	the	DT
cord-103204-gt6upfri	35	2	output	output	NN
cord-103204-gt6upfri	35	3	is	be	VBZ
cord-103204-gt6upfri	35	4	summarized	summarize	VBN
cord-103204-gt6upfri	35	5	in	in	IN
cord-103204-gt6upfri	35	6	T	T	NNP
cord-103204-gt6upfri	35	7	E	E	NNP
cord-103204-gt6upfri	35	8	X	X	NNP
cord-103204-gt6upfri	35	9	and	and	CC
cord-103204-gt6upfri	35	10	PDF	PDF	NNP
cord-103204-gt6upfri	35	11	format	format	NN
cord-103204-gt6upfri	35	12	and	and	CC
cord-103204-gt6upfri	35	13	visualized	visualize	VBD
cord-103204-gt6upfri	35	14	in	in	IN
cord-103204-gt6upfri	35	15	a	a	DT
cord-103204-gt6upfri	35	16	user	user	NN
cord-103204-gt6upfri	35	17	-	-	HYPH
cord-103204-gt6upfri	35	18	friendly	friendly	JJ
cord-103204-gt6upfri	35	19	HTML	html	NN
cord-103204-gt6upfri	35	20	page	page	NN
cord-103204-gt6upfri	35	21	,	,	,
cord-103204-gt6upfri	35	22	providing	provide	VBG
cord-103204-gt6upfri	35	23	access	access	NN
cord-103204-gt6upfri	35	24	to	to	IN
cord-103204-gt6upfri	35	25	all	all	DT
cord-103204-gt6upfri	35	26	results	result	NNS
cord-103204-gt6upfri	35	27	and	and	CC
cord-103204-gt6upfri	35	28	intermediate	intermediate	JJ
cord-103204-gt6upfri	35	29	files	file	NNS
cord-103204-gt6upfri	35	30	.	.	.
cord-103204-gt6upfri	36	1	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	36	2	comprises	comprise	VBZ
cord-103204-gt6upfri	36	3	an	an	DT
cord-103204-gt6upfri	36	4	assembly	assembly	NN
cord-103204-gt6upfri	36	5	of	of	IN
cord-103204-gt6upfri	36	6	different	different	JJ
cord-103204-gt6upfri	36	7	scripts	script	NNS
cord-103204-gt6upfri	36	8	and	and	CC
cord-103204-gt6upfri	36	9	tools	tool	NNS
cord-103204-gt6upfri	36	10	(	(	-LRB-
cord-103204-gt6upfri	36	11	Fig	fig	NN
cord-103204-gt6upfri	36	12	.	.	.
cord-103204-gt6upfri	36	13	1	1	CD
cord-103204-gt6upfri	36	14	)	)	-RRB-
cord-103204-gt6upfri	37	1	that	that	WDT
cord-103204-gt6upfri	37	2	allow	allow	VB
cord-103204-gt6upfri	37	3	for	for	IN
cord-103204-gt6upfri	37	4	the	the	DT
cord-103204-gt6upfri	37	5	detection	detection	NN
cord-103204-gt6upfri	37	6	of	of	IN
cord-103204-gt6upfri	37	7	recombination	recombination	NN
cord-103204-gt6upfri	37	8	and	and	CC
cord-103204-gt6upfri	37	9	positive	positive	JJ
cord-103204-gt6upfri	37	10	selection	selection	NN
cord-103204-gt6upfri	37	11	in	in	IN
cord-103204-gt6upfri	37	12	protein	protein	NN
cord-103204-gt6upfri	37	13	-	-	HYPH
cord-103204-gt6upfri	37	14	coding	code	VBG
cord-103204-gt6upfri	37	15	sequences	sequence	NNS
cord-103204-gt6upfri	37	16	.	.	.
cord-103204-gt6upfri	38	1	Each	each	DT
cord-103204-gt6upfri	38	2	third	third	JJ
cord-103204-gt6upfri	38	3	-	-	HYPH
cord-103204-gt6upfri	38	4	party	party	NN
cord-103204-gt6upfri	38	5	tool	tool	NN
cord-103204-gt6upfri	38	6	encapsulates	encapsulate	VBZ
cord-103204-gt6upfri	38	7	in	in	IN
cord-103204-gt6upfri	38	8	a	a	DT
cord-103204-gt6upfri	38	9	Docker	Docker	NNP
cord-103204-gt6upfri	38	10	container	container	NN
cord-103204-gt6upfri	38	11	and	and	CC
cord-103204-gt6upfri	38	12	all	all	DT
cord-103204-gt6upfri	38	13	steps	step	NNS
cord-103204-gt6upfri	38	14	are	be	VBP
cord-103204-gt6upfri	38	15	connected	connect	VBN
cord-103204-gt6upfri	38	16	in	in	IN
cord-103204-gt6upfri	38	17	a	a	DT
cord-103204-gt6upfri	38	18	Nextflow	Nextflow	NNP
cord-103204-gt6upfri	38	19	(	(	-LRB-
cord-103204-gt6upfri	38	20	Di	Di	NNP
cord-103204-gt6upfri	38	21	Tommaso	Tommaso	NNP
cord-103204-gt6upfri	38	22	et	et	FW
cord-103204-gt6upfri	38	23	al	al	NNP
cord-103204-gt6upfri	38	24	.	.	NNP
cord-103204-gt6upfri	38	25	,	,	,
cord-103204-gt6upfri	38	26	2017	2017	CD
cord-103204-gt6upfri	38	27	)	)	-RRB-
cord-103204-gt6upfri	38	28	implementation	implementation	NN
cord-103204-gt6upfri	38	29	for	for	IN
cord-103204-gt6upfri	38	30	full	full	JJ
cord-103204-gt6upfri	38	31	parallelization	parallelization	NN
cord-103204-gt6upfri	38	32	and	and	CC
cord-103204-gt6upfri	38	33	simple	simple	JJ
cord-103204-gt6upfri	38	34	execution	execution	NN
cord-103204-gt6upfri	38	35	.	.	.
cord-103204-gt6upfri	39	1	If	if	IN
cord-103204-gt6upfri	39	2	Nextflow	Nextflow	NNP
cord-103204-gt6upfri	39	3	and	and	CC
cord-103204-gt6upfri	39	4	Docker	Docker	NNP
cord-103204-gt6upfri	39	5	are	be	VBP
cord-103204-gt6upfri	39	6	configured	configure	VBN
cord-103204-gt6upfri	39	7	,	,	,
cord-103204-gt6upfri	39	8	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	39	9	can	can	MD
cord-103204-gt6upfri	39	10	be	be	VB
cord-103204-gt6upfri	39	11	installed	instal	VBN
cord-103204-gt6upfri	39	12	and	and	CC
cord-103204-gt6upfri	39	13	run	run	VBN
cord-103204-gt6upfri	39	14	with	with	IN
cord-103204-gt6upfri	39	15	a	a	DT
cord-103204-gt6upfri	39	16	single	single	JJ
cord-103204-gt6upfri	39	17	command	command	NN
cord-103204-gt6upfri	39	18	:	:	:
cord-103204-gt6upfri	39	19	nextflow	nextflow	NNP
cord-103204-gt6upfri	39	20	run	run	NNP
cord-103204-gt6upfri	40	1	hoelzer	hoelzer	NNP
cord-103204-gt6upfri	40	2	/	/	SYM
cord-103204-gt6upfri	40	3	poseidon	poseidon	NNP
cord-103204-gt6upfri	40	4	--help	--help	NNP
cord-103204-gt6upfri	40	5	.	.	.
cord-103204-gt6upfri	41	1	Different	different	JJ
cord-103204-gt6upfri	41	2	profiles	profile	NNS
cord-103204-gt6upfri	41	3	allow	allow	VBP
cord-103204-gt6upfri	41	4	the	the	DT
cord-103204-gt6upfri	41	5	reliable	reliable	JJ
cord-103204-gt6upfri	41	6	execution	execution	NN
cord-103204-gt6upfri	41	7	of	of	IN
cord-103204-gt6upfri	41	8	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	41	9	in	in	IN
cord-103204-gt6upfri	41	10	the	the	DT
cord-103204-gt6upfri	41	11	cloud	cloud	NN
cord-103204-gt6upfri	41	12	or	or	CC
cord-103204-gt6upfri	41	13	on	on	IN
cord-103204-gt6upfri	41	14	a	a	DT
cord-103204-gt6upfri	41	15	cluster	cluster	NN
cord-103204-gt6upfri	41	16	system	system	NN
cord-103204-gt6upfri	41	17	.	.	.
cord-103204-gt6upfri	42	1	Starting	start	VBG
cord-103204-gt6upfri	42	2	from	from	IN
cord-103204-gt6upfri	42	3	homologous	homologous	JJ
cord-103204-gt6upfri	42	4	coding	coding	NN
cord-103204-gt6upfri	42	5	sequences	sequence	NNS
cord-103204-gt6upfri	42	6	provided	provide	VBN
cord-103204-gt6upfri	42	7	by	by	IN
cord-103204-gt6upfri	42	8	the	the	DT
cord-103204-gt6upfri	42	9	user	user	NN
cord-103204-gt6upfri	42	10	,	,	,
cord-103204-gt6upfri	42	11	we	-PRON-	PRP
cord-103204-gt6upfri	42	12	build	build	VBP
cord-103204-gt6upfri	42	13	a	a	DT
cord-103204-gt6upfri	42	14	multiple	multiple	JJ
cord-103204-gt6upfri	42	15	sequence	sequence	NN
cord-103204-gt6upfri	42	16	alignment	alignment	NN
cord-103204-gt6upfri	42	17	guided	guide	VBN
cord-103204-gt6upfri	42	18	by	by	IN
cord-103204-gt6upfri	42	19	amino	amino	NN
cord-103204-gt6upfri	42	20	acid	acid	JJ
cord-103204-gt6upfri	42	21	information	information	NN
cord-103204-gt6upfri	42	22	with	with	IN
cord-103204-gt6upfri	42	23	TranslatorX	TranslatorX	NNP
cord-103204-gt6upfri	42	24	(	(	-LRB-
cord-103204-gt6upfri	42	25	v1.1	v1.1	NN
cord-103204-gt6upfri	42	26	)	)	-RRB-
cord-103204-gt6upfri	43	1	(	(	-LRB-
cord-103204-gt6upfri	43	2	Abascal	Abascal	NNP
cord-103204-gt6upfri	43	3	et	et	FW
cord-103204-gt6upfri	43	4	al	al	NNP
cord-103204-gt6upfri	43	5	.	.	NNP
cord-103204-gt6upfri	43	6	,	,	,
cord-103204-gt6upfri	43	7	2010	2010	CD
cord-103204-gt6upfri	43	8	)	)	-RRB-
cord-103204-gt6upfri	43	9	,	,	,
cord-103204-gt6upfri	43	10	using	use	VBG
cord-103204-gt6upfri	43	11	Muscle	Muscle	NNP
cord-103204-gt6upfri	43	12	(	(	-LRB-
cord-103204-gt6upfri	43	13	v3.8.31	v3.8.31	NNP
cord-103204-gt6upfri	43	14	)	)	-RRB-
cord-103204-gt6upfri	44	1	(	(	-LRB-
cord-103204-gt6upfri	44	2	Edgar	Edgar	NNP
cord-103204-gt6upfri	44	3	,	,	,
cord-103204-gt6upfri	44	4	2004	2004	CD
cord-103204-gt6upfri	44	5	)	)	-RRB-
cord-103204-gt6upfri	44	6	to	to	TO
cord-103204-gt6upfri	44	7	align	align	VB
cord-103204-gt6upfri	44	8	the	the	DT
cord-103204-gt6upfri	44	9	sequences	sequence	NNS
cord-103204-gt6upfri	44	10	.	.	.
cord-103204-gt6upfri	45	1	The	the	DT
cord-103204-gt6upfri	45	2	resulting	result	VBG
cord-103204-gt6upfri	45	3	in	in	IN
cord-103204-gt6upfri	45	4	-	-	HYPH
cord-103204-gt6upfri	45	5	frame	frame	NN
cord-103204-gt6upfri	45	6	nucleotide	nucleotide	JJ
cord-103204-gt6upfri	45	7	alignment	alignment	NN
cord-103204-gt6upfri	45	8	is	be	VBZ
cord-103204-gt6upfri	45	9	cleaned	clean	VBN
cord-103204-gt6upfri	45	10	for	for	IN
cord-103204-gt6upfri	45	11	Indels	Indels	NNPS
cord-103204-gt6upfri	45	12	.	.	.
cord-103204-gt6upfri	46	1	A	a	DT
cord-103204-gt6upfri	46	2	best	well	RBS
cord-103204-gt6upfri	46	3	-	-	HYPH
cord-103204-gt6upfri	46	4	fitting	fitting	JJ
cord-103204-gt6upfri	46	5	substitution	substitution	NN
cord-103204-gt6upfri	46	6	model	model	NN
cord-103204-gt6upfri	46	7	is	be	VBZ
cord-103204-gt6upfri	46	8	selected	select	VBN
cord-103204-gt6upfri	46	9	c	c	NN
cord-103204-gt6upfri	46	10	Oxford	Oxford	NNP
cord-103204-gt6upfri	46	11	University	University	NNP
cord-103204-gt6upfri	46	12	Press	Press	NNP
cord-103204-gt6upfri	46	13	2016	2016	CD
cord-103204-gt6upfri	46	14	.	.	.
cord-103204-gt6upfri	47	1	using	use	VBG
cord-103204-gt6upfri	47	2	MODELTEST	MODELTEST	NNP
cord-103204-gt6upfri	48	1	(	(	-LRB-
cord-103204-gt6upfri	48	2	Posada	Posada	NNP
cord-103204-gt6upfri	48	3	and	and	CC
cord-103204-gt6upfri	48	4	Crandall	Crandall	NNP
cord-103204-gt6upfri	48	5	,	,	,
cord-103204-gt6upfri	48	6	1998	1998	CD
cord-103204-gt6upfri	48	7	)	)	-RRB-
cord-103204-gt6upfri	48	8	,	,	,
cord-103204-gt6upfri	48	9	which	which	WDT
cord-103204-gt6upfri	48	10	is	be	VBZ
cord-103204-gt6upfri	48	11	part	part	NN
cord-103204-gt6upfri	48	12	of	of	IN
cord-103204-gt6upfri	48	13	the	the	DT
cord-103204-gt6upfri	48	14	HyPhy	HyPhy	NNP
cord-103204-gt6upfri	48	15	suite	suite	NN
cord-103204-gt6upfri	48	16	(	(	-LRB-
cord-103204-gt6upfri	48	17	v2.2.7	v2.2.7	NNP
cord-103204-gt6upfri	48	18	)	)	-RRB-
cord-103204-gt6upfri	49	1	(	(	-LRB-
cord-103204-gt6upfri	49	2	Pond	Pond	NNP
cord-103204-gt6upfri	49	3	et	et	NNP
cord-103204-gt6upfri	49	4	al	al	NNP
cord-103204-gt6upfri	49	5	.	.	NNP
cord-103204-gt6upfri	49	6	,	,	,
cord-103204-gt6upfri	49	7	2005	2005	CD
cord-103204-gt6upfri	49	8	)	)	-RRB-
cord-103204-gt6upfri	49	9	.	.	.
cord-103204-gt6upfri	50	1	Possible	possible	JJ
cord-103204-gt6upfri	50	2	recombination	recombination	NN
cord-103204-gt6upfri	50	3	events	event	NNS
cord-103204-gt6upfri	50	4	and	and	CC
cord-103204-gt6upfri	50	5	corresponding	correspond	VBG
cord-103204-gt6upfri	50	6	breakpoints	breakpoint	NNS
cord-103204-gt6upfri	50	7	in	in	IN
cord-103204-gt6upfri	50	8	the	the	DT
cord-103204-gt6upfri	50	9	alignment	alignment	NN
cord-103204-gt6upfri	50	10	are	be	VBP
cord-103204-gt6upfri	50	11	detected	detect	VBN
cord-103204-gt6upfri	50	12	using	use	VBG
cord-103204-gt6upfri	50	13	GARD	GARD	NNP
cord-103204-gt6upfri	50	14	(	(	-LRB-
cord-103204-gt6upfri	50	15	Pond	Pond	NNP
cord-103204-gt6upfri	50	16	et	et	NNP
cord-103204-gt6upfri	50	17	al	al	NNP
cord-103204-gt6upfri	50	18	.	.	NNP
cord-103204-gt6upfri	50	19	,	,	,
cord-103204-gt6upfri	50	20	2006b	2006b	CD
cord-103204-gt6upfri	50	21	,	,	,
cord-103204-gt6upfri	50	22	a	a	LS
cord-103204-gt6upfri	50	23	)	)	-RRB-
cord-103204-gt6upfri	50	24	under	under	IN
cord-103204-gt6upfri	50	25	the	the	DT
cord-103204-gt6upfri	50	26	previously	previously	RB
cord-103204-gt6upfri	50	27	selected	select	VBN
cord-103204-gt6upfri	50	28	substitution	substitution	NN
cord-103204-gt6upfri	50	29	model	model	NN
cord-103204-gt6upfri	50	30	.	.	.
cord-103204-gt6upfri	51	1	All	all	DT
cord-103204-gt6upfri	51	2	breakpoints	breakpoint	NNS
cord-103204-gt6upfri	51	3	are	be	VBP
cord-103204-gt6upfri	51	4	tested	test	VBN
cord-103204-gt6upfri	51	5	for	for	IN
cord-103204-gt6upfri	51	6	significant	significant	JJ
cord-103204-gt6upfri	51	7	topological	topological	JJ
cord-103204-gt6upfri	51	8	incongruence	incongruence	NN
cord-103204-gt6upfri	51	9	using	use	VBG
cord-103204-gt6upfri	51	10	a	a	DT
cord-103204-gt6upfri	51	11	Kashino	Kashino	NNP
cord-103204-gt6upfri	51	12	Hasegawa	Hasegawa	NNP
cord-103204-gt6upfri	51	13	(	(	-LRB-
cord-103204-gt6upfri	51	14	KH	KH	NNP
cord-103204-gt6upfri	51	15	)	)	-RRB-
cord-103204-gt6upfri	51	16	test	test	NN
cord-103204-gt6upfri	51	17	(	(	-LRB-
cord-103204-gt6upfri	51	18	Kishino	Kishino	NNP
cord-103204-gt6upfri	51	19	and	and	CC
cord-103204-gt6upfri	51	20	Hasegawa	Hasegawa	NNP
cord-103204-gt6upfri	51	21	,	,	,
cord-103204-gt6upfri	51	22	1989	1989	CD
cord-103204-gt6upfri	51	23	)	)	-RRB-
cord-103204-gt6upfri	51	24	.	.	.
cord-103204-gt6upfri	52	1	KHinsignificant	khinsignificant	JJ
cord-103204-gt6upfri	52	2	breakpoints	breakpoint	NNS
cord-103204-gt6upfri	52	3	most	most	RBS
cord-103204-gt6upfri	52	4	frequently	frequently	RB
cord-103204-gt6upfri	52	5	arise	arise	VBP
cord-103204-gt6upfri	52	6	from	from	IN
cord-103204-gt6upfri	52	7	variation	variation	NN
cord-103204-gt6upfri	52	8	in	in	IN
cord-103204-gt6upfri	52	9	branch	branch	NN
cord-103204-gt6upfri	52	10	lengths	length	NNS
cord-103204-gt6upfri	52	11	between	between	IN
cord-103204-gt6upfri	52	12	segments	segment	NNS
cord-103204-gt6upfri	52	13	.	.	.
cord-103204-gt6upfri	53	1	However	however	RB
cord-103204-gt6upfri	53	2	,	,	,
cord-103204-gt6upfri	53	3	we	-PRON-	PRP
cord-103204-gt6upfri	53	4	observed	observe	VBD
cord-103204-gt6upfri	53	5	interesting	interesting	JJ
cord-103204-gt6upfri	53	6	positively	positively	RB
cord-103204-gt6upfri	53	7	selected	select	VBN
cord-103204-gt6upfri	53	8	sites	site	NNS
cord-103204-gt6upfri	53	9	in	in	IN
cord-103204-gt6upfri	53	10	fragments	fragment	NNS
cord-103204-gt6upfri	53	11	without	without	IN
cord-103204-gt6upfri	53	12	any	any	DT
cord-103204-gt6upfri	53	13	significant	significant	JJ
cord-103204-gt6upfri	53	14	topological	topological	JJ
cord-103204-gt6upfri	53	15	incongruence	incongruence	NN
cord-103204-gt6upfri	53	16	(	(	-LRB-
cord-103204-gt6upfri	53	17	Fuchs	Fuchs	NNP
cord-103204-gt6upfri	53	18	et	et	FW
cord-103204-gt6upfri	53	19	al	al	NNP
cord-103204-gt6upfri	53	20	.	.	NNP
cord-103204-gt6upfri	53	21	,	,	,
cord-103204-gt6upfri	53	22	2017	2017	CD
cord-103204-gt6upfri	53	23	)	)	-RRB-
cord-103204-gt6upfri	53	24	.	.	.
cord-103204-gt6upfri	54	1	Thus	thus	RB
cord-103204-gt6upfri	54	2	,	,	,
cord-103204-gt6upfri	54	3	KH	kh	NN
cord-103204-gt6upfri	54	4	-	-	HYPH
cord-103204-gt6upfri	54	5	insignificant	insignificant	JJ
cord-103204-gt6upfri	54	6	breakpoints	breakpoint	NNS
cord-103204-gt6upfri	54	7	can	can	MD
cord-103204-gt6upfri	54	8	be	be	VB
cord-103204-gt6upfri	54	9	taken	take	VBN
cord-103204-gt6upfri	54	10	into	into	IN
cord-103204-gt6upfri	54	11	account	account	NN
cord-103204-gt6upfri	54	12	and	and	CC
cord-103204-gt6upfri	54	13	are	be	VBP
cord-103204-gt6upfri	54	14	marked	mark	VBN
cord-103204-gt6upfri	54	15	in	in	IN
cord-103204-gt6upfri	54	16	the	the	DT
cord-103204-gt6upfri	54	17	final	final	JJ
cord-103204-gt6upfri	54	18	output	output	NN
cord-103204-gt6upfri	54	19	,	,	,
cord-103204-gt6upfri	54	20	as	as	IN
cord-103204-gt6upfri	54	21	they	-PRON-	PRP
cord-103204-gt6upfri	54	22	might	may	MD
cord-103204-gt6upfri	54	23	not	not	RB
cord-103204-gt6upfri	54	24	occur	occur	VB
cord-103204-gt6upfri	54	25	from	from	IN
cord-103204-gt6upfri	54	26	real	real	JJ
cord-103204-gt6upfri	54	27	recombination	recombination	NN
cord-103204-gt6upfri	54	28	events	event	NNS
cord-103204-gt6upfri	54	29	.	.	.
cord-103204-gt6upfri	55	1	Positions	position	NNS
cord-103204-gt6upfri	55	2	of	of	IN
cord-103204-gt6upfri	55	3	putative	putative	JJ
cord-103204-gt6upfri	55	4	breakpoints	breakpoint	NNS
cord-103204-gt6upfri	55	5	that	that	WDT
cord-103204-gt6upfri	55	6	would	would	MD
cord-103204-gt6upfri	55	7	destroy	destroy	VB
cord-103204-gt6upfri	55	8	the	the	DT
cord-103204-gt6upfri	55	9	open	open	JJ
cord-103204-gt6upfri	55	10	reading	reading	NN
cord-103204-gt6upfri	55	11	frame	frame	NN
cord-103204-gt6upfri	55	12	are	be	VBP
cord-103204-gt6upfri	55	13	adjusted	adjust	VBN
cord-103204-gt6upfri	55	14	to	to	IN
cord-103204-gt6upfri	55	15	the	the	DT
cord-103204-gt6upfri	55	16	next	next	JJ
cord-103204-gt6upfri	55	17	valid	valid	JJ
cord-103204-gt6upfri	55	18	position	position	NN
cord-103204-gt6upfri	55	19	.	.	.
cord-103204-gt6upfri	56	1	Phylogenetic	phylogenetic	JJ
cord-103204-gt6upfri	56	2	reconstructions	reconstruction	NNS
cord-103204-gt6upfri	56	3	on	on	IN
cord-103204-gt6upfri	56	4	the	the	DT
cord-103204-gt6upfri	56	5	full	full	JJ
cord-103204-gt6upfri	56	6	alignment	alignment	NN
cord-103204-gt6upfri	56	7	and	and	CC
cord-103204-gt6upfri	56	8	all	all	DT
cord-103204-gt6upfri	56	9	fragments	fragment	NNS
cord-103204-gt6upfri	56	10	are	be	VBP
cord-103204-gt6upfri	56	11	performed	perform	VBN
cord-103204-gt6upfri	56	12	with	with	IN
cord-103204-gt6upfri	56	13	RAxML	RAxML	NNS
cord-103204-gt6upfri	56	14	(	(	-LRB-
cord-103204-gt6upfri	56	15	v8.2.12	v8.2.12	NN
cord-103204-gt6upfri	56	16	)	)	-RRB-
cord-103204-gt6upfri	56	17	(	(	-LRB-
cord-103204-gt6upfri	56	18	Stamatakis	Stamatakis	NNP
cord-103204-gt6upfri	56	19	,	,	,
cord-103204-gt6upfri	56	20	2014	2014	CD
cord-103204-gt6upfri	56	21	)	)	-RRB-
cord-103204-gt6upfri	56	22	using	use	VBG
cord-103204-gt6upfri	56	23	the	the	DT
cord-103204-gt6upfri	56	24	GTRGAMMA	GTRGAMMA	NNP
cord-103204-gt6upfri	56	25	model	model	NN
cord-103204-gt6upfri	56	26	for	for	IN
cord-103204-gt6upfri	56	27	nucleotide	nucleotide	JJ
cord-103204-gt6upfri	56	28	sequences	sequence	NNS
cord-103204-gt6upfri	56	29	and	and	CC
cord-103204-gt6upfri	56	30	PROTGAMMAWAG	PROTGAMMAWAG	NNP
cord-103204-gt6upfri	56	31	for	for	IN
cord-103204-gt6upfri	56	32	amino	amino	JJ
cord-103204-gt6upfri	56	33	acids	acid	NNS
cord-103204-gt6upfri	56	34	.	.	.
cord-103204-gt6upfri	57	1	All	all	DT
cord-103204-gt6upfri	57	2	calculations	calculation	NNS
cord-103204-gt6upfri	57	3	are	be	VBP
cord-103204-gt6upfri	57	4	performed	perform	VBN
cord-103204-gt6upfri	57	5	with	with	IN
cord-103204-gt6upfri	57	6	1	1	CD
cord-103204-gt6upfri	57	7	000	000	CD
cord-103204-gt6upfri	57	8	bootstrap	bootstrap	NN
cord-103204-gt6upfri	57	9	replicates	replicate	NNS
cord-103204-gt6upfri	57	10	.	.	.
cord-103204-gt6upfri	58	1	The	the	DT
cord-103204-gt6upfri	58	2	user	user	NN
cord-103204-gt6upfri	58	3	can	can	MD
cord-103204-gt6upfri	58	4	apply	apply	VB
cord-103204-gt6upfri	58	5	optional	optional	JJ
cord-103204-gt6upfri	58	6	outgroup	outgroup	NN
cord-103204-gt6upfri	58	7	rooting	rooting	NN
cord-103204-gt6upfri	58	8	.	.	.
cord-103204-gt6upfri	59	1	The	the	DT
cord-103204-gt6upfri	59	2	Newick	Newick	NNP
cord-103204-gt6upfri	59	3	Utilities	Utilities	NNPS
cord-103204-gt6upfri	59	4	suite	suite	NN
cord-103204-gt6upfri	59	5	(	(	-LRB-
cord-103204-gt6upfri	59	6	v1.6	v1.6	NNS
cord-103204-gt6upfri	59	7	)	)	-RRB-
cord-103204-gt6upfri	59	8	(	(	-LRB-
cord-103204-gt6upfri	59	9	Junier	Junier	NNP
cord-103204-gt6upfri	59	10	and	and	CC
cord-103204-gt6upfri	59	11	Zdobnov	Zdobnov	NNP
cord-103204-gt6upfri	59	12	,	,	,
cord-103204-gt6upfri	59	13	2010	2010	CD
cord-103204-gt6upfri	59	14	)	)	-RRB-
cord-103204-gt6upfri	59	15	is	be	VBZ
cord-103204-gt6upfri	59	16	used	use	VBN
cord-103204-gt6upfri	59	17	to	to	TO
cord-103204-gt6upfri	59	18	visualize	visualize	VB
cord-103204-gt6upfri	59	19	the	the	DT
cord-103204-gt6upfri	59	20	calculated	calculate	VBN
cord-103204-gt6upfri	59	21	trees	tree	NNS
cord-103204-gt6upfri	59	22	in	in	IN
cord-103204-gt6upfri	59	23	different	different	JJ
cord-103204-gt6upfri	59	24	formats	format	NNS
cord-103204-gt6upfri	59	25	.	.	.
cord-103204-gt6upfri	60	1	Positive	positive	JJ
cord-103204-gt6upfri	60	2	selection	selection	NN
cord-103204-gt6upfri	60	3	is	be	VBZ
cord-103204-gt6upfri	60	4	analyzed	analyze	VBN
cord-103204-gt6upfri	60	5	on	on	IN
cord-103204-gt6upfri	60	6	the	the	DT
cord-103204-gt6upfri	60	7	full	full	JJ
cord-103204-gt6upfri	60	8	alignment	alignment	NN
cord-103204-gt6upfri	60	9	and	and	CC
cord-103204-gt6upfri	60	10	each	each	DT
cord-103204-gt6upfri	60	11	of	of	IN
cord-103204-gt6upfri	60	12	the	the	DT
cord-103204-gt6upfri	60	13	fragments	fragment	NNS
cord-103204-gt6upfri	60	14	separately	separately	RB
cord-103204-gt6upfri	60	15	.	.	.
cord-103204-gt6upfri	61	1	Maximum	maximum	JJ
cord-103204-gt6upfri	61	2	-	-	HYPH
cord-103204-gt6upfri	61	3	likelihood	likelihood	NN
cord-103204-gt6upfri	61	4	tests	test	NNS
cord-103204-gt6upfri	61	5	to	to	TO
cord-103204-gt6upfri	61	6	detect	detect	VB
cord-103204-gt6upfri	61	7	positive	positive	JJ
cord-103204-gt6upfri	61	8	selection	selection	NN
cord-103204-gt6upfri	61	9	under	under	IN
cord-103204-gt6upfri	61	10	varying	vary	VBG
cord-103204-gt6upfri	61	11	site	site	NN
cord-103204-gt6upfri	61	12	models	model	NNS
cord-103204-gt6upfri	61	13	are	be	VBP
cord-103204-gt6upfri	61	14	performed	perform	VBN
cord-103204-gt6upfri	61	15	with	with	IN
cord-103204-gt6upfri	61	16	CODEML	CODEML	NNP
cord-103204-gt6upfri	61	17	(	(	-LRB-
cord-103204-gt6upfri	61	18	M1a	M1a	NNP
cord-103204-gt6upfri	61	19	vs.	vs.	IN
cord-103204-gt6upfri	61	20	M2a	M2a	NNP
cord-103204-gt6upfri	61	21	,	,	,
cord-103204-gt6upfri	61	22	M7	m7	NN
cord-103204-gt6upfri	61	23	vs.	vs.	FW
cord-103204-gt6upfri	61	24	M8	M8	NNP
cord-103204-gt6upfri	61	25	)	)	-RRB-
cord-103204-gt6upfri	61	26	implemented	implement	VBD
cord-103204-gt6upfri	61	27	within	within	IN
cord-103204-gt6upfri	61	28	the	the	DT
cord-103204-gt6upfri	61	29	PAML	PAML	NNP
cord-103204-gt6upfri	61	30	suite	suite	NN
cord-103204-gt6upfri	61	31	(	(	-LRB-
cord-103204-gt6upfri	61	32	v4.9	v4.9	NNP
cord-103204-gt6upfri	61	33	)	)	-RRB-
cord-103204-gt6upfri	61	34	(	(	-LRB-
cord-103204-gt6upfri	61	35	Yang	Yang	NNP
cord-103204-gt6upfri	61	36	,	,	,
cord-103204-gt6upfri	61	37	2007	2007	CD
cord-103204-gt6upfri	61	38	)	)	-RRB-
cord-103204-gt6upfri	61	39	.	.	.
cord-103204-gt6upfri	62	1	Furthermore	furthermore	RB
cord-103204-gt6upfri	62	2	,	,	,
cord-103204-gt6upfri	62	3	we	-PRON-	PRP
cord-103204-gt6upfri	62	4	implemented	implement	VBD
cord-103204-gt6upfri	62	5	the	the	DT
cord-103204-gt6upfri	62	6	M8a	M8a	NNP
cord-103204-gt6upfri	62	7	vs.	vs.	CC
cord-103204-gt6upfri	62	8	M8	m8	NN
cord-103204-gt6upfri	62	9	test	test	NN
cord-103204-gt6upfri	62	10	proposed	propose	VBN
cord-103204-gt6upfri	62	11	by	by	IN
cord-103204-gt6upfri	62	12	Swanson	Swanson	NNP
cord-103204-gt6upfri	62	13	et	et	NNP
cord-103204-gt6upfri	62	14	al	al	NNP
cord-103204-gt6upfri	62	15	.	.	.
cord-103204-gt6upfri	63	1	(	(	-LRB-
cord-103204-gt6upfri	63	2	2003	2003	CD
cord-103204-gt6upfri	63	3	)	)	-RRB-
cord-103204-gt6upfri	63	4	as	as	IN
cord-103204-gt6upfri	63	5	an	an	DT
cord-103204-gt6upfri	63	6	additional	additional	JJ
cord-103204-gt6upfri	63	7	model	model	NN
cord-103204-gt6upfri	63	8	test	test	NN
cord-103204-gt6upfri	63	9	in	in	IN
cord-103204-gt6upfri	63	10	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	63	11	.	.	.
cord-103204-gt6upfri	64	1	The	the	DT
cord-103204-gt6upfri	64	2	different	different	JJ
cord-103204-gt6upfri	64	3	statistical	statistical	JJ
cord-103204-gt6upfri	64	4	site	site	NN
cord-103204-gt6upfri	64	5	models	model	NNS
cord-103204-gt6upfri	64	6	that	that	WDT
cord-103204-gt6upfri	64	7	do	do	VBP
cord-103204-gt6upfri	64	8	not	not	RB
cord-103204-gt6upfri	64	9	allow	allow	VB
cord-103204-gt6upfri	64	10	(	(	-LRB-
cord-103204-gt6upfri	64	11	neutral	neutral	JJ
cord-103204-gt6upfri	64	12	models	model	NNS
cord-103204-gt6upfri	64	13	)	)	-RRB-
cord-103204-gt6upfri	64	14	or	or	CC
cord-103204-gt6upfri	64	15	allow	allow	VB
cord-103204-gt6upfri	64	16	(	(	-LRB-
cord-103204-gt6upfri	64	17	selection	selection	NN
cord-103204-gt6upfri	64	18	models	model	NNS
cord-103204-gt6upfri	64	19	)	)	-RRB-
cord-103204-gt6upfri	64	20	a	a	DT
cord-103204-gt6upfri	64	21	class	class	NN
cord-103204-gt6upfri	64	22	of	of	IN
cord-103204-gt6upfri	64	23	codons	codon	NNS
cord-103204-gt6upfri	64	24	to	to	TO
cord-103204-gt6upfri	64	25	evolve	evolve	VB
cord-103204-gt6upfri	64	26	with	with	IN
cord-103204-gt6upfri	64	27	ω	ω	NN
cord-103204-gt6upfri	64	28	>	>	XX
cord-103204-gt6upfri	65	1	1	1	CD
cord-103204-gt6upfri	65	2	are	be	VBP
cord-103204-gt6upfri	65	3	compared	compare	VBN
cord-103204-gt6upfri	65	4	.	.	.
cord-103204-gt6upfri	66	1	Furthermore	furthermore	RB
cord-103204-gt6upfri	66	2	,	,	,
cord-103204-gt6upfri	66	3	varying	vary	VBG
cord-103204-gt6upfri	66	4	codon	codon	NN
cord-103204-gt6upfri	66	5	frequency	frequency	NN
cord-103204-gt6upfri	66	6	models	model	NNS
cord-103204-gt6upfri	66	7	are	be	VBP
cord-103204-gt6upfri	66	8	applied	apply	VBN
cord-103204-gt6upfri	66	9	to	to	TO
cord-103204-gt6upfri	66	10	simulate	simulate	VB
cord-103204-gt6upfri	66	11	different	different	JJ
cord-103204-gt6upfri	66	12	nucleotide	nucleotide	JJ
cord-103204-gt6upfri	66	13	substitution	substitution	NN
cord-103204-gt6upfri	66	14	rates	rate	NNS
cord-103204-gt6upfri	66	15	.	.	.
cord-103204-gt6upfri	67	1	A	a	DT
cord-103204-gt6upfri	67	2	gene	gene	NN
cord-103204-gt6upfri	67	3	is	be	VBZ
cord-103204-gt6upfri	67	4	declared	declare	VBN
cord-103204-gt6upfri	67	5	to	to	TO
cord-103204-gt6upfri	67	6	be	be	VB
cord-103204-gt6upfri	67	7	positively	positively	RB
cord-103204-gt6upfri	67	8	selected	select	VBN
cord-103204-gt6upfri	67	9	if	if	IN
cord-103204-gt6upfri	67	10	the	the	DT
cord-103204-gt6upfri	67	11	neutral	neutral	JJ
cord-103204-gt6upfri	67	12	model	model	NN
cord-103204-gt6upfri	67	13	can	can	MD
cord-103204-gt6upfri	67	14	be	be	VB
cord-103204-gt6upfri	67	15	rejected	reject	VBN
cord-103204-gt6upfri	67	16	in	in	IN
cord-103204-gt6upfri	67	17	favor	favor	NN
cord-103204-gt6upfri	67	18	of	of	IN
cord-103204-gt6upfri	67	19	the	the	DT
cord-103204-gt6upfri	67	20	positive	positive	JJ
cord-103204-gt6upfri	67	21	selection	selection	NN
cord-103204-gt6upfri	67	22	model	model	NN
cord-103204-gt6upfri	67	23	based	base	VBN
cord-103204-gt6upfri	67	24	on	on	IN
cord-103204-gt6upfri	67	25	a	a	DT
cord-103204-gt6upfri	67	26	likelihood	likelihood	NN
cord-103204-gt6upfri	67	27	ratio	ratio	NN
cord-103204-gt6upfri	67	28	test	test	NN
cord-103204-gt6upfri	67	29	.	.	.
cord-103204-gt6upfri	68	1	Then	then	RB
cord-103204-gt6upfri	68	2	,	,	,
cord-103204-gt6upfri	68	3	a	a	DT
cord-103204-gt6upfri	68	4	Bayes	Bayes	NNP
cord-103204-gt6upfri	68	5	empirical	empirical	JJ
cord-103204-gt6upfri	68	6	Bayes	Bayes	NNP
cord-103204-gt6upfri	68	7	(	(	-LRB-
cord-103204-gt6upfri	68	8	BEB	BEB	NNP
cord-103204-gt6upfri	68	9	)	)	-RRB-
cord-103204-gt6upfri	68	10	approach	approach	NN
cord-103204-gt6upfri	69	1	(	(	-LRB-
cord-103204-gt6upfri	69	2	Yang	Yang	NNP
cord-103204-gt6upfri	69	3	et	et	NNP
cord-103204-gt6upfri	69	4	al	al	NNP
cord-103204-gt6upfri	69	5	.	.	NNP
cord-103204-gt6upfri	69	6	,	,	,
cord-103204-gt6upfri	69	7	2005	2005	CD
cord-103204-gt6upfri	69	8	)	)	-RRB-
cord-103204-gt6upfri	69	9	is	be	VBZ
cord-103204-gt6upfri	69	10	applied	apply	VBN
cord-103204-gt6upfri	69	11	to	to	TO
cord-103204-gt6upfri	69	12	calculate	calculate	VB
cord-103204-gt6upfri	69	13	posterior	posterior	JJ
cord-103204-gt6upfri	69	14	probabilities	probability	NNS
cord-103204-gt6upfri	69	15	(	(	-LRB-
cord-103204-gt6upfri	69	16	P	p	NN
cord-103204-gt6upfri	69	17	P	p	NN
cord-103204-gt6upfri	69	18	)	)	-RRB-
cord-103204-gt6upfri	69	19	that	that	IN
cord-103204-gt6upfri	69	20	a	a	DT
cord-103204-gt6upfri	69	21	codon	codon	NN
cord-103204-gt6upfri	69	22	comes	come	VBZ
cord-103204-gt6upfri	69	23	from	from	IN
cord-103204-gt6upfri	69	24	the	the	DT
cord-103204-gt6upfri	69	25	site	site	NN
cord-103204-gt6upfri	69	26	class	class	NN
cord-103204-gt6upfri	69	27	with	with	IN
cord-103204-gt6upfri	69	28	ω	ω	ADD
cord-103204-gt6upfri	70	1	>	>	XX
cord-103204-gt6upfri	70	2	1	1	CD
cord-103204-gt6upfri	70	3	.	.	.
cord-103204-gt6upfri	71	1	Positively	positively	RB
cord-103204-gt6upfri	71	2	selected	select	VBN
cord-103204-gt6upfri	71	3	sites	site	NNS
cord-103204-gt6upfri	71	4	with	with	IN
cord-103204-gt6upfri	71	5	an	an	DT
cord-103204-gt6upfri	71	6	assigned	assigned	JJ
cord-103204-gt6upfri	71	7	P	p	NN
cord-103204-gt6upfri	71	8	P	p	NN
cord-103204-gt6upfri	71	9	>	>	XX
cord-103204-gt6upfri	71	10	0.95	0.95	CD
cord-103204-gt6upfri	71	11	are	be	VBP
cord-103204-gt6upfri	71	12	depicted	depict	VBN
cord-103204-gt6upfri	71	13	as	as	IN
cord-103204-gt6upfri	71	14	significant	significant	JJ
cord-103204-gt6upfri	71	15	.	.	.
cord-103204-gt6upfri	72	1	We	-PRON-	PRP
cord-103204-gt6upfri	72	2	graphically	graphically	RB
cord-103204-gt6upfri	72	3	summarize	summarize	VBP
cord-103204-gt6upfri	72	4	all	all	DT
cord-103204-gt6upfri	72	5	positively	positively	RB
cord-103204-gt6upfri	72	6	selected	select	VBN
cord-103204-gt6upfri	72	7	sites	site	NNS
cord-103204-gt6upfri	72	8	under	under	IN
cord-103204-gt6upfri	72	9	varying	vary	VBG
cord-103204-gt6upfri	72	10	frequency	frequency	NN
cord-103204-gt6upfri	72	11	models	model	NNS
cord-103204-gt6upfri	72	12	in	in	IN
cord-103204-gt6upfri	72	13	the	the	DT
cord-103204-gt6upfri	72	14	output	output	NN
cord-103204-gt6upfri	72	15	(	(	-LRB-
cord-103204-gt6upfri	72	16	Fig	Fig	NNP
cord-103204-gt6upfri	72	17	.	.	.
cord-103204-gt6upfri	72	18	1	1	CD
cord-103204-gt6upfri	72	19	)	)	-RRB-
cord-103204-gt6upfri	72	20	.	.	.
cord-103204-gt6upfri	73	1	Thus	thus	RB
cord-103204-gt6upfri	73	2	,	,	,
cord-103204-gt6upfri	73	3	we	-PRON-	PRP
cord-103204-gt6upfri	73	4	allow	allow	VBP
cord-103204-gt6upfri	73	5	the	the	DT
cord-103204-gt6upfri	73	6	user	user	NN
cord-103204-gt6upfri	73	7	to	to	TO
cord-103204-gt6upfri	73	8	investigate	investigate	VB
cord-103204-gt6upfri	73	9	sites	site	NNS
cord-103204-gt6upfri	73	10	that	that	WDT
cord-103204-gt6upfri	73	11	would	would	MD
cord-103204-gt6upfri	73	12	be	be	VB
cord-103204-gt6upfri	73	13	dismissed	dismiss	VBN
cord-103204-gt6upfri	73	14	from	from	IN
cord-103204-gt6upfri	73	15	the	the	DT
cord-103204-gt6upfri	73	16	output	output	NN
cord-103204-gt6upfri	73	17	when	when	WRB
cord-103204-gt6upfri	73	18	using	use	VBG
cord-103204-gt6upfri	73	19	a	a	DT
cord-103204-gt6upfri	73	20	P	p	NN
cord-103204-gt6upfri	73	21	P	p	NN
cord-103204-gt6upfri	73	22	threshold	threshold	NN
cord-103204-gt6upfri	73	23	.	.	.
cord-103204-gt6upfri	74	1	For	for	IN
cord-103204-gt6upfri	74	2	example	example	NN
cord-103204-gt6upfri	74	3	,	,	,
cord-103204-gt6upfri	74	4	such	such	JJ
cord-103204-gt6upfri	74	5	sites	site	NNS
cord-103204-gt6upfri	74	6	could	could	MD
cord-103204-gt6upfri	74	7	be	be	VB
cord-103204-gt6upfri	74	8	located	locate	VBN
cord-103204-gt6upfri	74	9	in	in	IN
cord-103204-gt6upfri	74	10	regulatory	regulatory	JJ
cord-103204-gt6upfri	74	11	domains	domain	NNS
cord-103204-gt6upfri	74	12	of	of	IN
cord-103204-gt6upfri	74	13	the	the	DT
cord-103204-gt6upfri	74	14	final	final	JJ
cord-103204-gt6upfri	74	15	protein	protein	NN
cord-103204-gt6upfri	74	16	,	,	,
cord-103204-gt6upfri	74	17	yielding	yield	VBG
cord-103204-gt6upfri	74	18	a	a	DT
cord-103204-gt6upfri	74	19	lower	low	JJR
cord-103204-gt6upfri	74	20	P	p	NN
cord-103204-gt6upfri	74	21	P	p	NN
cord-103204-gt6upfri	74	22	value	value	NN
cord-103204-gt6upfri	74	23	due	due	IN
cord-103204-gt6upfri	74	24	to	to	IN
cord-103204-gt6upfri	74	25	insufficient	insufficient	JJ
cord-103204-gt6upfri	74	26	species	species	NN
cord-103204-gt6upfri	74	27	sampling	sampling	NN
cord-103204-gt6upfri	74	28	(	(	-LRB-
cord-103204-gt6upfri	74	29	McBee	McBee	NNP
cord-103204-gt6upfri	74	30	et	et	NNP
cord-103204-gt6upfri	74	31	al	al	NNP
cord-103204-gt6upfri	74	32	.	.	NNP
cord-103204-gt6upfri	74	33	,	,	,
cord-103204-gt6upfri	74	34	2015	2015	CD
cord-103204-gt6upfri	74	35	)	)	-RRB-
cord-103204-gt6upfri	74	36	.	.	.
cord-103204-gt6upfri	75	1	The	the	DT
cord-103204-gt6upfri	75	2	final	final	JJ
cord-103204-gt6upfri	75	3	output	output	NN
cord-103204-gt6upfri	75	4	of	of	IN
cord-103204-gt6upfri	75	5	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	75	6	is	be	VBZ
cord-103204-gt6upfri	75	7	based	base	VBN
cord-103204-gt6upfri	75	8	on	on	IN
cord-103204-gt6upfri	75	9	a	a	DT
cord-103204-gt6upfri	75	10	heavily	heavily	RB
cord-103204-gt6upfri	75	11	modified	modify	VBN
cord-103204-gt6upfri	75	12	version	version	NN
cord-103204-gt6upfri	75	13	of	of	IN
cord-103204-gt6upfri	75	14	the	the	DT
cord-103204-gt6upfri	75	15	TranslatorX	TranslatorX	NNP
cord-103204-gt6upfri	75	16	HTML	html	NN
cord-103204-gt6upfri	75	17	output	output	NN
cord-103204-gt6upfri	75	18	.	.	.
cord-103204-gt6upfri	76	1	The	the	DT
cord-103204-gt6upfri	76	2	amino	amino	NN
cord-103204-gt6upfri	76	3	acid	acid	NN
cord-103204-gt6upfri	76	4	color	color	NN
cord-103204-gt6upfri	76	5	code	code	NN
cord-103204-gt6upfri	76	6	is	be	VBZ
cord-103204-gt6upfri	76	7	adapted	adapt	VBN
cord-103204-gt6upfri	76	8	from	from	IN
cord-103204-gt6upfri	76	9	TranslatorX.	TranslatorX.	NNS
cord-103204-gt6upfri	77	1	Here	here	RB
cord-103204-gt6upfri	77	2	we	-PRON-	PRP
cord-103204-gt6upfri	77	3	present	present	VBP
cord-103204-gt6upfri	77	4	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	77	5	,	,	,
cord-103204-gt6upfri	77	6	an	an	DT
cord-103204-gt6upfri	77	7	easy	easy	JJ
cord-103204-gt6upfri	77	8	-	-	HYPH
cord-103204-gt6upfri	77	9	to	to	TO
cord-103204-gt6upfri	77	10	-	-	HYPH
cord-103204-gt6upfri	77	11	use	use	NN
cord-103204-gt6upfri	77	12	Nextflow	Nextflow	NNP
cord-103204-gt6upfri	77	13	pipeline	pipeline	NN
cord-103204-gt6upfri	77	14	for	for	IN
cord-103204-gt6upfri	77	15	the	the	DT
cord-103204-gt6upfri	77	16	accurate	accurate	JJ
cord-103204-gt6upfri	77	17	detection	detection	NN
cord-103204-gt6upfri	77	18	of	of	IN
cord-103204-gt6upfri	77	19	site	site	NN
cord-103204-gt6upfri	77	20	-	-	HYPH
cord-103204-gt6upfri	77	21	specific	specific	JJ
cord-103204-gt6upfri	77	22	positive	positive	JJ
cord-103204-gt6upfri	77	23	selection	selection	NN
cord-103204-gt6upfri	77	24	and	and	CC
cord-103204-gt6upfri	77	25	recombination	recombination	NN
cord-103204-gt6upfri	77	26	events	event	NNS
cord-103204-gt6upfri	77	27	in	in	IN
cord-103204-gt6upfri	77	28	protein	protein	NN
cord-103204-gt6upfri	77	29	-	-	HYPH
cord-103204-gt6upfri	77	30	coding	code	VBG
cord-103204-gt6upfri	77	31	sequences	sequence	NNS
cord-103204-gt6upfri	77	32	.	.	.
cord-103204-gt6upfri	78	1	The	the	DT
cord-103204-gt6upfri	78	2	input	input	NN
cord-103204-gt6upfri	78	3	is	be	VBZ
cord-103204-gt6upfri	78	4	a	a	DT
cord-103204-gt6upfri	78	5	multiple	multiple	JJ
cord-103204-gt6upfri	78	6	FASTA	FASTA	NNP
cord-103204-gt6upfri	78	7	file	file	NN
cord-103204-gt6upfri	78	8	of	of	IN
cord-103204-gt6upfri	78	9	homologous	homologous	JJ
cord-103204-gt6upfri	78	10	coding	coding	NN
cord-103204-gt6upfri	78	11	sequences	sequence	NNS
cord-103204-gt6upfri	78	12	that	that	WDT
cord-103204-gt6upfri	78	13	is	be	VBZ
cord-103204-gt6upfri	78	14	automatically	automatically	RB
cord-103204-gt6upfri	78	15	transferred	transfer	VBN
cord-103204-gt6upfri	78	16	into	into	IN
cord-103204-gt6upfri	78	17	a	a	DT
cord-103204-gt6upfri	78	18	codon	codon	NN
cord-103204-gt6upfri	78	19	-	-	HYPH
cord-103204-gt6upfri	78	20	based	base	VBN
cord-103204-gt6upfri	78	21	alignment	alignment	NN
cord-103204-gt6upfri	78	22	.	.	.
cord-103204-gt6upfri	79	1	Since	since	IN
cord-103204-gt6upfri	79	2	recombination	recombination	NN
cord-103204-gt6upfri	79	3	can	can	MD
cord-103204-gt6upfri	79	4	have	have	VB
cord-103204-gt6upfri	79	5	a	a	DT
cord-103204-gt6upfri	79	6	profound	profound	JJ
cord-103204-gt6upfri	79	7	impact	impact	NN
cord-103204-gt6upfri	79	8	on	on	IN
cord-103204-gt6upfri	79	9	the	the	DT
cord-103204-gt6upfri	79	10	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	79	11	history	history	NN
cord-103204-gt6upfri	79	12	of	of	IN
cord-103204-gt6upfri	79	13	sequences	sequence	NNS
cord-103204-gt6upfri	79	14	,	,	,
cord-103204-gt6upfri	79	15	we	-PRON-	PRP
cord-103204-gt6upfri	79	16	initially	initially	RB
cord-103204-gt6upfri	79	17	check	check	VBP
cord-103204-gt6upfri	79	18	the	the	DT
cord-103204-gt6upfri	79	19	alignment	alignment	NN
cord-103204-gt6upfri	79	20	for	for	IN
cord-103204-gt6upfri	79	21	topological	topological	JJ
cord-103204-gt6upfri	79	22	incongruence	incongruence	NN
cord-103204-gt6upfri	79	23	to	to	TO
cord-103204-gt6upfri	79	24	define	define	VB
cord-103204-gt6upfri	79	25	putative	putative	JJ
cord-103204-gt6upfri	79	26	recombination	recombination	NN
cord-103204-gt6upfri	79	27	breakpoints	breakpoint	NNS
cord-103204-gt6upfri	79	28	.	.	.
cord-103204-gt6upfri	80	1	The	the	DT
cord-103204-gt6upfri	80	2	whole	whole	JJ
cord-103204-gt6upfri	80	3	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	80	4	analysis	analysis	NN
cord-103204-gt6upfri	80	5	of	of	IN
cord-103204-gt6upfri	80	6	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	80	7	is	be	VBZ
cord-103204-gt6upfri	80	8	performed	perform	VBN
cord-103204-gt6upfri	80	9	independently	independently	RB
cord-103204-gt6upfri	80	10	for	for	IN
cord-103204-gt6upfri	80	11	the	the	DT
cord-103204-gt6upfri	80	12	full	full	JJ
cord-103204-gt6upfri	80	13	alignment	alignment	NN
cord-103204-gt6upfri	80	14	and	and	CC
cord-103204-gt6upfri	80	15	all	all	DT
cord-103204-gt6upfri	80	16	possible	possible	JJ
cord-103204-gt6upfri	80	17	fragments	fragment	NNS
cord-103204-gt6upfri	80	18	.	.	.
cord-103204-gt6upfri	81	1	PoSeiDon	PoSeiDon	NNP
cord-103204-gt6upfri	81	2	automatically	automatically	RB
cord-103204-gt6upfri	81	3	calculates	calculate	VBZ
cord-103204-gt6upfri	81	4	maximum	maximum	JJ
cord-103204-gt6upfri	81	5	likelihood	likelihood	NN
cord-103204-gt6upfri	81	6	-	-	HYPH
cord-103204-gt6upfri	81	7	based	base	VBN
cord-103204-gt6upfri	81	8	phylogenetic	phylogenetic	NN
cord-103204-gt6upfri	81	9	trees	tree	NNS
cord-103204-gt6upfri	81	10	for	for	IN
cord-103204-gt6upfri	81	11	all	all	DT
cord-103204-gt6upfri	81	12	alignments	alignment	NNS
cord-103204-gt6upfri	81	13	,	,	,
cord-103204-gt6upfri	81	14	estimates	estimate	VBZ
cord-103204-gt6upfri	81	15	ω	ω	NN
cord-103204-gt6upfri	81	16	values	value	NNS
cord-103204-gt6upfri	81	17	at	at	IN
cord-103204-gt6upfri	81	18	each	each	DT
cord-103204-gt6upfri	81	19	site	site	NN
cord-103204-gt6upfri	81	20	,	,	,
cord-103204-gt6upfri	81	21	and	and	CC
cord-103204-gt6upfri	81	22	computes	compute	VBZ
cord-103204-gt6upfri	81	23	their	-PRON-	PRP$
cord-103204-gt6upfri	81	24	impact	impact	NN
cord-103204-gt6upfri	81	25	on	on	IN
cord-103204-gt6upfri	81	26	the	the	DT
cord-103204-gt6upfri	81	27	positive	positive	JJ
cord-103204-gt6upfri	81	28	selection	selection	NN
cord-103204-gt6upfri	81	29	.	.	.
cord-103204-gt6upfri	82	1	All	all	DT
cord-103204-gt6upfri	82	2	identified	identify	VBN
cord-103204-gt6upfri	82	3	sites	site	NNS
cord-103204-gt6upfri	82	4	and	and	CC
cord-103204-gt6upfri	82	5	their	-PRON-	PRP$
cord-103204-gt6upfri	82	6	significance	significance	NN
cord-103204-gt6upfri	82	7	values	value	NNS
cord-103204-gt6upfri	82	8	are	be	VBP
cord-103204-gt6upfri	82	9	projected	project	VBN
cord-103204-gt6upfri	82	10	onto	onto	IN
cord-103204-gt6upfri	82	11	the	the	DT
cord-103204-gt6upfri	82	12	codon	codon	NN
cord-103204-gt6upfri	82	13	and	and	CC
cord-103204-gt6upfri	82	14	amino	amino	NN
cord-103204-gt6upfri	82	15	acid	acid	NN
cord-103204-gt6upfri	82	16	alignment	alignment	NN
cord-103204-gt6upfri	82	17	of	of	IN
cord-103204-gt6upfri	82	18	the	the	DT
cord-103204-gt6upfri	82	19	input	input	NN
cord-103204-gt6upfri	82	20	sequences	sequence	NNS
cord-103204-gt6upfri	82	21	to	to	TO
cord-103204-gt6upfri	82	22	allow	allow	VB
cord-103204-gt6upfri	82	23	visual	visual	JJ
cord-103204-gt6upfri	82	24	identification	identification	NN
cord-103204-gt6upfri	82	25	of	of	IN
cord-103204-gt6upfri	82	26	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	82	27	hot	hot	JJ
cord-103204-gt6upfri	82	28	-	-	HYPH
cord-103204-gt6upfri	82	29	spots	spot	NNS
cord-103204-gt6upfri	82	30	with	with	IN
cord-103204-gt6upfri	82	31	high	high	JJ
cord-103204-gt6upfri	82	32	ω	ω	CD
cord-103204-gt6upfri	82	33	values	value	NNS
cord-103204-gt6upfri	82	34	.	.	.
cord-103204-gt6upfri	83	1	Additionally	additionally	RB
cord-103204-gt6upfri	83	2	,	,	,
cord-103204-gt6upfri	83	3	publication	publication	NN
cord-103204-gt6upfri	83	4	-	-	HYPH
cord-103204-gt6upfri	83	5	ready	ready	JJ
cord-103204-gt6upfri	83	6	PDF	PDF	NNP
cord-103204-gt6upfri	83	7	and	and	CC
cord-103204-gt6upfri	83	8	L	L	NNP
cord-103204-gt6upfri	83	9	A	A	NNP
cord-103204-gt6upfri	83	10	T	t	NN
cord-103204-gt6upfri	83	11	E	e	NN
cord-103204-gt6upfri	83	12	X	x	NN
cord-103204-gt6upfri	83	13	tables	table	NNS
cord-103204-gt6upfri	83	14	are	be	VBP
cord-103204-gt6upfri	83	15	provided	provide	VBN
cord-103204-gt6upfri	83	16	,	,	,
cord-103204-gt6upfri	83	17	including	include	VBG
cord-103204-gt6upfri	83	18	all	all	DT
cord-103204-gt6upfri	83	19	breakpoints	breakpoint	NNS
cord-103204-gt6upfri	83	20	and	and	CC
cord-103204-gt6upfri	83	21	significantly	significantly	RB
cord-103204-gt6upfri	83	22	positively	positively	RB
cord-103204-gt6upfri	83	23	selected	select	VBN
cord-103204-gt6upfri	83	24	sites	site	NNS
cord-103204-gt6upfri	83	25	.	.	.
cord-103204-gt6upfri	84	1	All	all	DT
cord-103204-gt6upfri	84	2	results	result	NNS
cord-103204-gt6upfri	84	3	are	be	VBP
cord-103204-gt6upfri	84	4	summarized	summarize	VBN
cord-103204-gt6upfri	84	5	in	in	IN
cord-103204-gt6upfri	84	6	a	a	DT
cord-103204-gt6upfri	84	7	userfriendly	userfriendly	JJ
cord-103204-gt6upfri	84	8	and	and	CC
cord-103204-gt6upfri	84	9	clear	clear	JJ
cord-103204-gt6upfri	84	10	manner	manner	NN
cord-103204-gt6upfri	84	11	,	,	,
cord-103204-gt6upfri	84	12	allowing	allow	VBG
cord-103204-gt6upfri	84	13	researchers	researcher	NNS
cord-103204-gt6upfri	84	14	to	to	TO
cord-103204-gt6upfri	84	15	study	study	VB
cord-103204-gt6upfri	84	16	positive	positive	JJ
cord-103204-gt6upfri	84	17	selection	selection	NN
cord-103204-gt6upfri	84	18	.	.	.
cord-103204-gt6upfri	85	1	Funding	funding	NN
cord-103204-gt6upfri	85	2	:	:	:
cord-103204-gt6upfri	86	1	This	this	DT
cord-103204-gt6upfri	86	2	work	work	NN
cord-103204-gt6upfri	86	3	has	have	VBZ
cord-103204-gt6upfri	86	4	been	be	VBN
cord-103204-gt6upfri	86	5	supported	support	VBN
cord-103204-gt6upfri	86	6	by	by	IN
cord-103204-gt6upfri	86	7	the	the	DT
cord-103204-gt6upfri	86	8	Deutsche	Deutsche	NNP
cord-103204-gt6upfri	86	9	Forschungsgemeinschaft	Forschungsgemeinschaft	NNP
cord-103204-gt6upfri	86	10	(	(	-LRB-
cord-103204-gt6upfri	86	11	DFG	DFG	NNP
cord-103204-gt6upfri	86	12	)	)	-RRB-
cord-103204-gt6upfri	86	13	through	through	IN
cord-103204-gt6upfri	86	14	the	the	DT
cord-103204-gt6upfri	86	15	Priority	Priority	NNP
cord-103204-gt6upfri	86	16	Program	Program	NNP
cord-103204-gt6upfri	87	1	SPP-1596	SPP-1596	NNP
cord-103204-gt6upfri	88	1	MA5082/7	MA5082/7	NNP
cord-103204-gt6upfri	88	2	-	-	SYM
cord-103204-gt6upfri	88	3	1	1	CD
cord-103204-gt6upfri	89	1	and	and	CC
cord-103204-gt6upfri	89	2	was	be	VBD
cord-103204-gt6upfri	89	3	partly	partly	RB
cord-103204-gt6upfri	89	4	conducted	conduct	VBN
cord-103204-gt6upfri	89	5	within	within	IN
cord-103204-gt6upfri	89	6	the	the	DT
cord-103204-gt6upfri	89	7	Collaborative	Collaborative	NNP
cord-103204-gt6upfri	89	8	Research	Research	NNP
cord-103204-gt6upfri	89	9	Centre	Centre	NNP
cord-103204-gt6upfri	89	10	AquaDiva	AquaDiva	NNP
cord-103204-gt6upfri	89	11	(	(	-LRB-
cord-103204-gt6upfri	89	12	CRC	CRC	NNP
cord-103204-gt6upfri	89	13	1076	1076	CD
cord-103204-gt6upfri	89	14	AquaDiva	AquaDiva	NNP
cord-103204-gt6upfri	89	15	)	)	-RRB-
cord-103204-gt6upfri	89	16	of	of	IN
cord-103204-gt6upfri	89	17	the	the	DT
cord-103204-gt6upfri	89	18	Friedrich	Friedrich	NNP
cord-103204-gt6upfri	89	19	Schiller	Schiller	NNP
cord-103204-gt6upfri	89	20	University	University	NNP
cord-103204-gt6upfri	89	21	Jena	Jena	NNP
cord-103204-gt6upfri	89	22	,	,	,
cord-103204-gt6upfri	89	23	also	also	RB
cord-103204-gt6upfri	89	24	funded	fund	VBN
cord-103204-gt6upfri	89	25	by	by	IN
cord-103204-gt6upfri	89	26	the	the	DT
cord-103204-gt6upfri	89	27	DFG	DFG	NNP
cord-103204-gt6upfri	89	28	.	.	.
cord-103204-gt6upfri	90	1	MH	MH	NNP
cord-103204-gt6upfri	90	2	appreciates	appreciate	VBZ
cord-103204-gt6upfri	90	3	the	the	DT
cord-103204-gt6upfri	90	4	support	support	NN
cord-103204-gt6upfri	90	5	of	of	IN
cord-103204-gt6upfri	90	6	the	the	DT
cord-103204-gt6upfri	90	7	Joachim	Joachim	NNP
cord-103204-gt6upfri	90	8	Herz	Herz	NNP
cord-103204-gt6upfri	90	9	Foundation	Foundation	NNP
cord-103204-gt6upfri	90	10	by	by	IN
cord-103204-gt6upfri	90	11	the	the	DT
cord-103204-gt6upfri	90	12	addon	addon	NN
cord-103204-gt6upfri	90	13	fellowship	fellowship	NN
cord-103204-gt6upfri	90	14	for	for	IN
cord-103204-gt6upfri	90	15	interdisciplinary	interdisciplinary	JJ
cord-103204-gt6upfri	90	16	life	life	NN
cord-103204-gt6upfri	90	17	science	science	NN
cord-103204-gt6upfri	90	18	.	.	.
cord-103204-gt6upfri	91	1	We	-PRON-	PRP
cord-103204-gt6upfri	91	2	would	would	MD
cord-103204-gt6upfri	91	3	like	like	VB
cord-103204-gt6upfri	91	4	to	to	TO
cord-103204-gt6upfri	91	5	thank	thank	VB
cord-103204-gt6upfri	91	6	Lasse	Lasse	NNP
cord-103204-gt6upfri	91	7	Faber	Faber	NNP
cord-103204-gt6upfri	91	8	for	for	IN
cord-103204-gt6upfri	91	9	his	-PRON-	PRP$
cord-103204-gt6upfri	91	10	help	help	NN
cord-103204-gt6upfri	91	11	in	in	IN
cord-103204-gt6upfri	91	12	implementing	implement	VBG
cord-103204-gt6upfri	91	13	the	the	DT
cord-103204-gt6upfri	91	14	Dockers	Dockers	NNPS
cord-103204-gt6upfri	91	15	.	.	.
cord-103204-gt6upfri	92	1	Conflict	conflict	NN
cord-103204-gt6upfri	92	2	of	of	IN
cord-103204-gt6upfri	92	3	Interest	interest	NN
cord-103204-gt6upfri	92	4	:	:	:
cord-103204-gt6upfri	93	1	none	none	NN
cord-103204-gt6upfri	93	2	declared	declare	VBD
cord-103204-gt6upfri	93	3	.	.	.
cord-103204-gt6upfri	93	4	 	 	_SP
cord-103204-gt6upfri	94	1	TranslatorX	TranslatorX	NNP
cord-103204-gt6upfri	94	2	:	:	:
cord-103204-gt6upfri	95	1	multiple	multiple	JJ
cord-103204-gt6upfri	95	2	alignment	alignment	NN
cord-103204-gt6upfri	95	3	of	of	IN
cord-103204-gt6upfri	95	4	nucleotide	nucleotide	JJ
cord-103204-gt6upfri	95	5	sequences	sequence	NNS
cord-103204-gt6upfri	95	6	guided	guide	VBN
cord-103204-gt6upfri	95	7	by	by	IN
cord-103204-gt6upfri	95	8	amino	amino	NN
cord-103204-gt6upfri	95	9	acid	acid	JJ
cord-103204-gt6upfri	95	10	translations	translation	NNS
cord-103204-gt6upfri	96	1	Datamonkey	Datamonkey	NNP
cord-103204-gt6upfri	96	2	2010	2010	CD
cord-103204-gt6upfri	96	3	:	:	:
cord-103204-gt6upfri	96	4	a	a	DT
cord-103204-gt6upfri	96	5	suite	suite	NN
cord-103204-gt6upfri	96	6	of	of	IN
cord-103204-gt6upfri	96	7	phylogenetic	phylogenetic	JJ
cord-103204-gt6upfri	96	8	analysis	analysis	NN
cord-103204-gt6upfri	96	9	tools	tool	NNS
cord-103204-gt6upfri	96	10	for	for	IN
cord-103204-gt6upfri	96	11	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	96	12	biology	biology	NN
cord-103204-gt6upfri	97	1	Nextflow	Nextflow	NNP
cord-103204-gt6upfri	97	2	enables	enable	VBZ
cord-103204-gt6upfri	97	3	reproducible	reproducible	JJ
cord-103204-gt6upfri	97	4	computational	computational	JJ
cord-103204-gt6upfri	97	5	workflows	workflow	NNS
cord-103204-gt6upfri	97	6	Selecton	Selecton	NNP
cord-103204-gt6upfri	97	7	:	:	:
cord-103204-gt6upfri	97	8	a	a	DT
cord-103204-gt6upfri	97	9	server	server	NN
cord-103204-gt6upfri	97	10	for	for	IN
cord-103204-gt6upfri	97	11	detecting	detect	VBG
cord-103204-gt6upfri	97	12	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	97	13	forces	force	NNS
cord-103204-gt6upfri	97	14	at	at	IN
cord-103204-gt6upfri	97	15	a	a	DT
cord-103204-gt6upfri	97	16	single	single	JJ
cord-103204-gt6upfri	97	17	amino	amino	NN
cord-103204-gt6upfri	97	18	-	-	HYPH
cord-103204-gt6upfri	97	19	acid	acid	NN
cord-103204-gt6upfri	97	20	site	site	NN
cord-103204-gt6upfri	97	21	MUSCLE	muscle	NN
cord-103204-gt6upfri	97	22	:	:	:
cord-103204-gt6upfri	98	1	multiple	multiple	JJ
cord-103204-gt6upfri	98	2	sequence	sequence	NN
cord-103204-gt6upfri	98	3	alignment	alignment	NN
cord-103204-gt6upfri	98	4	with	with	IN
cord-103204-gt6upfri	98	5	high	high	JJ
cord-103204-gt6upfri	98	6	accuracy	accuracy	NN
cord-103204-gt6upfri	98	7	and	and	CC
cord-103204-gt6upfri	98	8	high	high	JJ
cord-103204-gt6upfri	98	9	throughput	throughput	NN
cord-103204-gt6upfri	98	10	Evolution	evolution	NN
cord-103204-gt6upfri	98	11	and	and	CC
cord-103204-gt6upfri	98	12	antiviral	antiviral	JJ
cord-103204-gt6upfri	98	13	specificities	specificity	NNS
cord-103204-gt6upfri	98	14	of	of	IN
cord-103204-gt6upfri	98	15	interferon	interferon	NN
cord-103204-gt6upfri	98	16	-	-	HYPH
cord-103204-gt6upfri	98	17	induced	induce	VBN
cord-103204-gt6upfri	98	18	Mx	Mx	NNP
cord-103204-gt6upfri	98	19	proteins	protein	NNS
cord-103204-gt6upfri	98	20	of	of	IN
cord-103204-gt6upfri	98	21	bats	bat	NNS
cord-103204-gt6upfri	98	22	against	against	IN
cord-103204-gt6upfri	98	23	Ebola	Ebola	NNP
cord-103204-gt6upfri	98	24	,	,	,
cord-103204-gt6upfri	98	25	Influenza	Influenza	NNP
cord-103204-gt6upfri	98	26	,	,	,
cord-103204-gt6upfri	98	27	and	and	CC
cord-103204-gt6upfri	98	28	other	other	JJ
cord-103204-gt6upfri	98	29	RNA	RNA	NNP
cord-103204-gt6upfri	98	30	viruses	virus	NNS
cord-103204-gt6upfri	99	1	Signatures	signature	NNS
cord-103204-gt6upfri	99	2	of	of	IN
cord-103204-gt6upfri	99	3	environmental	environmental	JJ
cord-103204-gt6upfri	99	4	genetic	genetic	JJ
cord-103204-gt6upfri	99	5	adaptation	adaptation	NN
cord-103204-gt6upfri	99	6	pinpoint	pinpoint	NN
cord-103204-gt6upfri	99	7	pathogens	pathogen	NNS
cord-103204-gt6upfri	99	8	as	as	IN
cord-103204-gt6upfri	99	9	the	the	DT
cord-103204-gt6upfri	99	10	main	main	JJ
cord-103204-gt6upfri	99	11	selective	selective	JJ
cord-103204-gt6upfri	99	12	pressure	pressure	NN
cord-103204-gt6upfri	99	13	through	through	IN
cord-103204-gt6upfri	99	14	human	human	JJ
cord-103204-gt6upfri	99	15	evolution	evolution	NN
cord-103204-gt6upfri	100	1	The	the	DT
cord-103204-gt6upfri	100	2	Newick	Newick	NNP
cord-103204-gt6upfri	100	3	utilities	utility	NNS
cord-103204-gt6upfri	100	4	:	:	:
cord-103204-gt6upfri	100	5	high	high	JJ
cord-103204-gt6upfri	100	6	-	-	HYPH
cord-103204-gt6upfri	100	7	throughput	throughput	NN
cord-103204-gt6upfri	100	8	phylogenetic	phylogenetic	NN
cord-103204-gt6upfri	100	9	tree	tree	NN
cord-103204-gt6upfri	100	10	processing	process	VBG
cord-103204-gt6upfri	100	11	in	in	IN
cord-103204-gt6upfri	100	12	the	the	DT
cord-103204-gt6upfri	100	13	UNIX	UNIX	NNP
cord-103204-gt6upfri	100	14	shell	shell	NN
cord-103204-gt6upfri	100	15	Evaluation	Evaluation	NNP
cord-103204-gt6upfri	100	16	of	of	IN
cord-103204-gt6upfri	100	17	the	the	DT
cord-103204-gt6upfri	100	18	maximum	maximum	JJ
cord-103204-gt6upfri	100	19	likelihood	likelihood	NN
cord-103204-gt6upfri	100	20	estimate	estimate	NN
cord-103204-gt6upfri	100	21	of	of	IN
cord-103204-gt6upfri	100	22	the	the	DT
cord-103204-gt6upfri	100	23	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	100	24	tree	tree	NN
cord-103204-gt6upfri	100	25	topologies	topology	NNS
cord-103204-gt6upfri	100	26	from	from	IN
cord-103204-gt6upfri	100	27	DNA	dna	NN
cord-103204-gt6upfri	100	28	sequence	sequence	NN
cord-103204-gt6upfri	100	29	data	data	NN
cord-103204-gt6upfri	100	30	,	,	,
cord-103204-gt6upfri	100	31	and	and	CC
cord-103204-gt6upfri	100	32	the	the	DT
cord-103204-gt6upfri	100	33	branching	branch	VBG
cord-103204-gt6upfri	100	34	order	order	NN
cord-103204-gt6upfri	100	35	in	in	IN
cord-103204-gt6upfri	100	36	Hominoidea	Hominoidea	NNP
cord-103204-gt6upfri	101	1	The	the	DT
cord-103204-gt6upfri	101	2	Effect	Effect	NNP
cord-103204-gt6upfri	101	3	of	of	IN
cord-103204-gt6upfri	101	4	Species	Species	NNP
cord-103204-gt6upfri	101	5	Representation	Representation	NNP
cord-103204-gt6upfri	101	6	on	on	IN
cord-103204-gt6upfri	101	7	the	the	DT
cord-103204-gt6upfri	101	8	Detection	Detection	NNP
cord-103204-gt6upfri	101	9	of	of	IN
cord-103204-gt6upfri	101	10	Positive	Positive	NNP
cord-103204-gt6upfri	101	11	Selection	Selection	NNP
cord-103204-gt6upfri	101	12	in	in	IN
cord-103204-gt6upfri	101	13	Primate	Primate	NNP
cord-103204-gt6upfri	101	14	Gene	Gene	NNP
cord-103204-gt6upfri	101	15	Data	Data	NNP
cord-103204-gt6upfri	101	16	Sets	set	VBZ
cord-103204-gt6upfri	101	17	HyPhy	HyPhy	NNP
cord-103204-gt6upfri	101	18	:	:	:
cord-103204-gt6upfri	102	1	hypothesis	hypothesis	NN
cord-103204-gt6upfri	102	2	testing	testing	NN
cord-103204-gt6upfri	102	3	using	use	VBG
cord-103204-gt6upfri	102	4	phylogenies	phylogeny	NNS
cord-103204-gt6upfri	102	5	Automated	automate	VBN
cord-103204-gt6upfri	102	6	phylogenetic	phylogenetic	JJ
cord-103204-gt6upfri	102	7	detection	detection	NN
cord-103204-gt6upfri	102	8	of	of	IN
cord-103204-gt6upfri	102	9	recombination	recombination	NN
cord-103204-gt6upfri	102	10	using	use	VBG
cord-103204-gt6upfri	102	11	a	a	DT
cord-103204-gt6upfri	102	12	genetic	genetic	JJ
cord-103204-gt6upfri	102	13	algorithm	algorithm	NN
cord-103204-gt6upfri	102	14	GARD	GARD	NNP
cord-103204-gt6upfri	102	15	:	:	:
cord-103204-gt6upfri	102	16	a	a	DT
cord-103204-gt6upfri	102	17	genetic	genetic	JJ
cord-103204-gt6upfri	102	18	algorithm	algorithm	NN
cord-103204-gt6upfri	102	19	for	for	IN
cord-103204-gt6upfri	102	20	recombination	recombination	NN
cord-103204-gt6upfri	102	21	detection	detection	NN
cord-103204-gt6upfri	102	22	MODELTEST	MODELTEST	NNP
cord-103204-gt6upfri	102	23	:	:	:
cord-103204-gt6upfri	102	24	testing	test	VBG
cord-103204-gt6upfri	102	25	the	the	DT
cord-103204-gt6upfri	102	26	model	model	NN
cord-103204-gt6upfri	102	27	of	of	IN
cord-103204-gt6upfri	102	28	DNA	dna	NN
cord-103204-gt6upfri	102	29	substitution	substitution	NN
cord-103204-gt6upfri	102	30	Potential	potential	JJ
cord-103204-gt6upfri	102	31	impact	impact	NN
cord-103204-gt6upfri	102	32	of	of	IN
cord-103204-gt6upfri	102	33	recombination	recombination	NN
cord-103204-gt6upfri	102	34	on	on	IN
cord-103204-gt6upfri	102	35	sitewise	sitewise	NN
cord-103204-gt6upfri	102	36	approaches	approach	NNS
cord-103204-gt6upfri	102	37	for	for	IN
cord-103204-gt6upfri	102	38	detecting	detect	VBG
cord-103204-gt6upfri	102	39	positive	positive	JJ
cord-103204-gt6upfri	102	40	natural	natural	JJ
cord-103204-gt6upfri	102	41	selection	selection	NN
cord-103204-gt6upfri	102	42	RAxML	RAxML	VBZ
cord-103204-gt6upfri	102	43	version	version	NN
cord-103204-gt6upfri	102	44	8	8	CD
cord-103204-gt6upfri	102	45	:	:	:
cord-103204-gt6upfri	102	46	a	a	DT
cord-103204-gt6upfri	102	47	tool	tool	NN
cord-103204-gt6upfri	102	48	for	for	IN
cord-103204-gt6upfri	102	49	phylogenetic	phylogenetic	JJ
cord-103204-gt6upfri	102	50	analysis	analysis	NN
cord-103204-gt6upfri	102	51	and	and	CC
cord-103204-gt6upfri	102	52	postanalysis	postanalysis	NN
cord-103204-gt6upfri	102	53	of	of	IN
cord-103204-gt6upfri	102	54	large	large	JJ
cord-103204-gt6upfri	102	55	phylogenies	phylogeny	NNS
cord-103204-gt6upfri	102	56	Selecton	Selecton	NNP
cord-103204-gt6upfri	102	57	2007	2007	CD
cord-103204-gt6upfri	102	58	:	:	:
cord-103204-gt6upfri	102	59	advanced	advanced	JJ
cord-103204-gt6upfri	102	60	models	model	NNS
cord-103204-gt6upfri	102	61	for	for	IN
cord-103204-gt6upfri	102	62	detecting	detect	VBG
cord-103204-gt6upfri	102	63	positive	positive	JJ
cord-103204-gt6upfri	102	64	and	and	CC
cord-103204-gt6upfri	102	65	purifying	purify	VBG
cord-103204-gt6upfri	102	66	selection	selection	NN
cord-103204-gt6upfri	102	67	using	use	VBG
cord-103204-gt6upfri	102	68	a	a	DT
cord-103204-gt6upfri	102	69	Bayesian	bayesian	JJ
cord-103204-gt6upfri	102	70	inference	inference	NN
cord-103204-gt6upfri	102	71	approach	approach	NN
cord-103204-gt6upfri	102	72	PSP	PSP	NNP
cord-103204-gt6upfri	102	73	:	:	:
cord-103204-gt6upfri	102	74	rapid	rapid	JJ
cord-103204-gt6upfri	102	75	identification	identification	NN
cord-103204-gt6upfri	102	76	of	of	IN
cord-103204-gt6upfri	102	77	orthologous	orthologous	JJ
cord-103204-gt6upfri	102	78	coding	code	VBG
cord-103204-gt6upfri	102	79	genes	gene	NNS
cord-103204-gt6upfri	102	80	under	under	IN
cord-103204-gt6upfri	102	81	positive	positive	JJ
cord-103204-gt6upfri	102	82	selection	selection	NN
cord-103204-gt6upfri	102	83	across	across	IN
cord-103204-gt6upfri	102	84	multiple	multiple	JJ
cord-103204-gt6upfri	102	85	closely	closely	RB
cord-103204-gt6upfri	102	86	related	related	JJ
cord-103204-gt6upfri	102	87	prokaryotic	prokaryotic	JJ
cord-103204-gt6upfri	102	88	genomes	genome	NNS
cord-103204-gt6upfri	102	89	Pervasive	pervasive	JJ
cord-103204-gt6upfri	102	90	adaptive	adaptive	JJ
cord-103204-gt6upfri	102	91	evolution	evolution	NN
cord-103204-gt6upfri	102	92	in	in	IN
cord-103204-gt6upfri	102	93	mammalian	mammalian	JJ
cord-103204-gt6upfri	102	94	fertilization	fertilization	NN
cord-103204-gt6upfri	102	95	proteins	protein	NNS
cord-103204-gt6upfri	102	96	Detecting	detect	VBG
cord-103204-gt6upfri	102	97	natural	natural	JJ
cord-103204-gt6upfri	102	98	selection	selection	NN
cord-103204-gt6upfri	102	99	in	in	IN
cord-103204-gt6upfri	102	100	genomic	genomic	JJ
cord-103204-gt6upfri	102	101	data	datum	NNS
cord-103204-gt6upfri	102	102	VESPA	vespa	NN
cord-103204-gt6upfri	102	103	:	:	:
cord-103204-gt6upfri	102	104	very	very	RB
cord-103204-gt6upfri	102	105	large	large	JJ
cord-103204-gt6upfri	102	106	-	-	HYPH
cord-103204-gt6upfri	102	107	scale	scale	NN
cord-103204-gt6upfri	102	108	evolutionary	evolutionary	JJ
cord-103204-gt6upfri	102	109	and	and	CC
cord-103204-gt6upfri	102	110	selective	selective	JJ
cord-103204-gt6upfri	102	111	pressure	pressure	NN
cord-103204-gt6upfri	102	112	analyses	analysis	NNS
cord-103204-gt6upfri	102	113	PAML	PAML	NNP
cord-103204-gt6upfri	102	114	4	4	CD
cord-103204-gt6upfri	102	115	:	:	:
cord-103204-gt6upfri	103	1	phylogenetic	phylogenetic	JJ
cord-103204-gt6upfri	103	2	analysis	analysis	NN
cord-103204-gt6upfri	103	3	by	by	IN
cord-103204-gt6upfri	103	4	maximum	maximum	JJ
cord-103204-gt6upfri	103	5	likelihood	likelihood	NN
cord-103204-gt6upfri	104	1	Bayes	Bayes	NNP
cord-103204-gt6upfri	104	2	Empirical	Empirical	NNP
cord-103204-gt6upfri	104	3	Bayes	Bayes	NNP
cord-103204-gt6upfri	104	4	Inference	Inference	NNP
cord-103204-gt6upfri	104	5	of	of	IN
cord-103204-gt6upfri	104	6	Amino	Amino	NNP
cord-103204-gt6upfri	104	7	Acid	acid	NN
cord-103204-gt6upfri	104	8	Sites	site	NNS
cord-103204-gt6upfri	104	9	Under	under	IN
cord-103204-gt6upfri	104	10	Positive	positive	JJ
cord-103204-gt6upfri	104	11	Selection	selection	NN