#---------------------Start--------------------
#Configuration file of PartitionFinder2 
#Data: cp-reduced
#Note: each coding gene was divided into three independent data blocks according to 1st, 2nd, 3rd codon position.
#All RNA genes (tRNA and rRNA), intergenic spacers and introns were treated as three independent data blocks seperately.

alignment = cp_reduced.phy;

branchlengths = linked;

models = all;

model_selection = aicc;

[data_blocks]
accD_1=1-1527\3;
accD_2=2-1527\3;
accD_3=3-1527\3;
atpA_1=1528-3060\3;
atpA_2=1529-3060\3;
atpA_3=1530-3060\3;
atpB_1=3061-4557\3;
atpB_2=3062-4557\3;
atpB_3=3063-4557\3;
atpE_1=4558-4962\3;
atpE_2=4559-4962\3;
atpE_3=4560-4962\3;
atpF_1=4963-5517\3;
atpF_2=4964-5517\3;
atpF_3=4965-5517\3;
atpH_1=5518-5763\3;
atpH_2=5519-5763\3;
atpH_3=5520-5763\3;
atpI_1=5764-6507\3;
atpI_2=5765-6507\3;
atpI_3=5766-6507\3;
ccsA_1=6508-7461\3;
ccsA_2=6509-7461\3;
ccsA_3=6510-7461\3;
cemA_1=7462-8160\3;
cemA_2=7463-8160\3;
cemA_3=7464-8160\3;
clpP_1=8161-8769\3;
clpP_2=8162-8769\3;
clpP_3=8163-8769\3;
infA_1=8770-9003\3;
infA_2=8771-9003\3;
infA_3=8772-9003\3;
intergenic=9004-74867;
intron=74868-89107;
lhbA_1=89108-89296\3;
lhbA_2=89109-89296\3;
lhbA_3=89110-89296\3;
matK_1=89297-90856\3;
matK_2=89298-90856\3;
matK_3=89299-90856\3;
ndhA_1=90857-91948\3;
ndhA_2=90858-91948\3;
ndhA_3=90859-91948\3;
ndhB_1=91949-93478\3;
ndhB_2=91950-93478\3;
ndhB_3=91951-93478\3;
ndhC_1=93479-93841\3;
ndhC_2=93480-93841\3;
ndhC_3=93481-93841\3;
ndhD_1=93842-95377\3;
ndhD_2=93843-95377\3;
ndhD_3=93844-95377\3;
ndhE_1=95378-95683\3;
ndhE_2=95379-95683\3;
ndhE_3=95380-95683\3;
ndhF_1=95684-97929\3;
ndhF_2=95685-97929\3;
ndhF_3=95686-97929\3;
ndhG_1=97930-98460\3;
ndhG_2=97931-98460\3;
ndhG_3=97932-98460\3;
ndhH_1=98461-99642\3;
ndhH_2=98462-99642\3;
ndhH_3=98463-99642\3;
ndhI_1=99643-100185\3;
ndhI_2=99644-100185\3;
ndhI_3=99645-100185\3;
ndhJ_1=100186-100662\3;
ndhJ_2=100187-100662\3;
ndhJ_3=100188-100662\3;
ndhK_1=100663-101547\3;
ndhK_2=100664-101547\3;
ndhK_3=100665-101547\3;
petA_1=101548-102510\3;
petA_2=101549-102510\3;
petA_3=101550-102510\3;
petB_1=102511-103158\3;
petB_2=102512-103158\3;
petB_3=102513-103158\3;
petD_1=103159-103647\3;
petD_2=103160-103647\3;
petD_3=103161-103647\3;
petG_1=103648-103761\3;
petG_2=103649-103761\3;
petG_3=103650-103761\3;
petL_1=103762-103857\3;
petL_2=103763-103857\3;
petL_3=103764-103857\3;
petN_1=103858-103947\3;
petN_2=103859-103947\3;
petN_3=103860-103947\3;
psaA_1=103948-106200\3;
psaA_2=103949-106200\3;
psaA_3=103950-106200\3;
psaB_1=106201-108405\3;
psaB_2=106202-108405\3;
psaB_3=106203-108405\3;
psaC_1=108406-108651\3;
psaC_2=108407-108651\3;
psaC_3=108408-108651\3;
psaI_1=108652-108762\3;
psaI_2=108653-108762\3;
psaI_3=108654-108762\3;
psaJ_1=108763-108897\3;
psaJ_2=108764-108897\3;
psaJ_3=108765-108897\3;
psbA_1=108898-109959\3;
psbA_2=108899-109959\3;
psbA_3=108900-109959\3;
psbB_1=109960-111486\3;
psbB_2=109961-111486\3;
psbB_3=109962-111486\3;
psbC_1=111487-112908\3;
psbC_2=111488-112908\3;
psbC_3=111489-112908\3;
psbD_1=112909-113970\3;
psbD_2=112910-113970\3;
psbD_3=112911-113970\3;
psbE_1=113971-114222\3;
psbE_2=113972-114222\3;
psbE_3=113973-114222\3;
psbF_1=114223-114342\3;
psbF_2=114224-114342\3;
psbF_3=114225-114342\3;
psbH_1=114343-114564\3;
psbH_2=114344-114564\3;
psbH_3=114345-114564\3;
psbI_1=114565-114748\3;
psbI_2=114566-114748\3;
psbI_3=114567-114748\3;
psbJ_1=114749-114871\3;
psbJ_2=114750-114871\3;
psbJ_3=114751-114871\3;
psbK_1=114872-115051\3;
psbK_2=114873-115051\3;
psbK_3=114874-115051\3;
psbL_1=115052-115180\3;
psbL_2=115053-115180\3;
psbL_3=115054-115180\3;
psbM_1=115181-115285\3;
psbM_2=115182-115285\3;
psbM_3=115183-115285\3;
psbN_1=115286-115417\3;
psbN_2=115287-115417\3;
psbN_3=115288-115417\3;
psbT_1=115418-115525\3;
psbT_2=115419-115525\3;
psbT_3=115420-115525\3;
rbcL_1=115526-116953\3;
rbcL_2=115527-116953\3;
rbcL_3=115528-116953\3;
RNA=116954-123847;
rpl14_1=123848-124216\3;
rpl14_2=123849-124216\3;
rpl14_3=123850-124216\3;
rpl16_1=124217-124624\3;
rpl16_2=124218-124624\3;
rpl16_3=124219-124624\3;
rpl2_1=125397-126251\3;
rpl2_2=125398-126251\3;
rpl2_3=125399-126251\3;
rpl20_1=124625-125026\3;
rpl20_2=124626-125026\3;
rpl20_3=124627-125026\3;
rpl23=125027-125396;
rpl32_1=126252-126431\3;
rpl32_2=126253-126431\3;
rpl32_3=126254-126431\3;
rpl33_1=126432-126632\3;
rpl33_2=126433-126632\3;
rpl33_3=126434-126632\3;
rpl36_1=126633-126746\3;
rpl36_2=126634-126746\3;
rpl36_3=126635-126746\3;
rpoA_1=126747-127817\3;
rpoA_2=126748-127817\3;
rpoA_3=126749-127817\3;
rpoB_1=127818-131000\3;
rpoB_2=127819-131000\3;
rpoB_3=127820-131000\3;
rpoC1_1=131001-133058\3;
rpoC1_2=131002-133058\3;
rpoC1_3=131003-133058\3;
rpoC2_1=133059-137255\3;
rpoC2_2=133060-137255\3;
rpoC2_3=133061-137255\3;
rps11_1=137256-137672\3;
rps11_2=137257-137672\3;
rps11_3=137258-137672\3;
rps12_1=137673-138045\3;
rps12_2=137674-138045\3;
rps12_3=137675-138045\3;
rps14_1=138046-138348\3;
rps14_2=138047-138348\3;
rps14_3=138048-138348\3;
rps15_1=138349-138615\3;
rps15_2=138350-138615\3;
rps15_3=138351-138615\3;
rps16_1=138616-138885\3;
rps16_2=138617-138885\3;
rps16_3=138618-138885\3;
rps18_1=138886-139200\3;
rps18_2=138887-139200\3;
rps18_3=138888-139200\3;
rps19_1=139201-139479\3;
rps19_2=139202-139479\3;
rps19_3=139203-139479\3;
rps2_1=139480-140190\3;
rps2_2=139481-140190\3;
rps2_3=139482-140190\3;
rps3_1=140191-140853\3;
rps3_2=140192-140853\3;
rps3_3=140193-140853\3;
rps4_1=140854-141459\3;
rps4_2=140855-141459\3;
rps4_3=140856-141459\3;
rps7_1=141460-141927\3;
rps7_2=141461-141927\3;
rps7_3=141462-141927\3;
rps8_1=141928-142326\3;
rps8_2=141929-142326\3;
rps8_3=141930-142326\3;
ycf1_1=142327-148188\3;
ycf1_2=142328-148188\3;
ycf1_3=142329-148188\3;
ycf2_1=148189-155439\3;
ycf2_2=148190-155439\3;
ycf2_3=148191-155439\3;
ycf3_1=155440-155952\3;
ycf3_2=155441-155952\3;
ycf3_3=155442-155952\3;
ycf4_1=155953-156507\3;
ycf4_2=155954-156507\3;
ycf4_3=155955-156507\3;

[schemes]
search = rcluster;
#-----------------------END------------------------

#-----------------------Start----------------------
#Configuration file of PartitionFinder2 
#Data: Coding genes (CDS)
#Note: each coding gene was divided into three independent data blocks according to 1st, 2nd, 3rd codon position.


alignment = CDS.phy;

branchlengths = linked;

models = all;

model_selection = aicc;

[data_blocks]
accD=1-1527\3;
accD=2-1527\3;
accD=3-1527\3;
atpA=1528-3060\3;
atpA=1529-3060\3;
atpA=1530-3060\3;
atpB=3061-4557\3;
atpB=3062-4557\3;
atpB=3063-4557\3;
atpE=4558-4962\3;
atpE=4559-4962\3;
atpE=4560-4962\3;
atpF=4963-5517\3;
atpF=4964-5517\3;
atpF=4965-5517\3;
atpH=5518-5763\3;
atpH=5519-5763\3;
atpH=5520-5763\3;
atpI=5764-6507\3;
atpI=5765-6507\3;
atpI=5766-6507\3;
ccsA=6508-7461\3;
ccsA=6509-7461\3;
ccsA=6510-7461\3;
cemA=7462-8160\3;
cemA=7463-8160\3;
cemA=7464-8160\3;
clpP=8161-8769\3;
clpP=8162-8769\3;
clpP=8163-8769\3;
infA=8770-9003\3;
infA=8771-9003\3;
infA=8772-9003\3;
lhbA=9004-9192\3;
lhbA=9005-9192\3;
lhbA=9006-9192\3;
matK=9193-10752\3;
matK=9194-10752\3;
matK=9195-10752\3;
ndhA=10753-11844\3;
ndhA=10754-11844\3;
ndhA=10755-11844\3;
ndhB=11845-13374\3;
ndhB=11846-13374\3;
ndhB=11847-13374\3;
ndhC=13375-13737\3;
ndhC=13376-13737\3;
ndhC=13377-13737\3;
ndhD=13738-15273\3;
ndhD=13739-15273\3;
ndhD=13740-15273\3;
ndhE=15274-15579\3;
ndhE=15275-15579\3;
ndhE=15276-15579\3;
ndhF=15580-17825\3;
ndhF=15581-17825\3;
ndhF=15582-17825\3;
ndhG=17826-18356\3;
ndhG=17827-18356\3;
ndhG=17828-18356\3;
ndhH=18357-19538\3;
ndhH=18358-19538\3;
ndhH=18359-19538\3;
ndhI=19539-20081\3;
ndhI=19540-20081\3;
ndhI=19541-20081\3;
ndhJ=20082-20558\3;
ndhJ=20083-20558\3;
ndhJ=20084-20558\3;
ndhK=20559-21443\3;
ndhK=20560-21443\3;
ndhK=20561-21443\3;
petA=21444-22406\3;
petA=21445-22406\3;
petA=21446-22406\3;
petB=22407-23054\3;
petB=22408-23054\3;
petB=22409-23054\3;
petD=23055-23543\3;
petD=23056-23543\3;
petD=23057-23543\3;
petG=23544-23657\3;
petG=23545-23657\3;
petG=23546-23657\3;
petL=23658-23753\3;
petL=23659-23753\3;
petL=23660-23753\3;
petN=23754-23843\3;
petN=23755-23843\3;
petN=23756-23843\3;
psaA=23844-26096\3;
psaA=23845-26096\3;
psaA=23846-26096\3;
psaB=26097-28301\3;
psaB=26098-28301\3;
psaB=26099-28301\3;
psaC=28302-28547\3;
psaC=28303-28547\3;
psaC=28304-28547\3;
psaI=28548-28658\3;
psaI=28549-28658\3;
psaI=28550-28658\3;
psaJ=28659-28793\3;
psaJ=28660-28793\3;
psaJ=28661-28793\3;
psbA=28794-29855\3;
psbA=28795-29855\3;
psbA=28796-29855\3;
psbB=29856-31382\3;
psbB=29857-31382\3;
psbB=29858-31382\3;
psbC=31383-32804\3;
psbC=31384-32804\3;
psbC=31385-32804\3;
psbD=32805-33866\3;
psbD=32806-33866\3;
psbD=32807-33866\3;
psbE=33867-34118\3;
psbE=33868-34118\3;
psbE=33869-34118\3;
psbF=34119-34238\3;
psbF=34120-34238\3;
psbF=34121-34238\3;
psbH=34239-34460\3;
psbH=34240-34460\3;
psbH=34241-34460\3;
psbI=34461-34644\3;
psbI=34462-34644\3;
psbI=34463-34644\3;
psbJ=34645-34767\3;
psbJ=34646-34767\3;
psbJ=34647-34767\3;
psbK=34768-34947\3;
psbK=34769-34947\3;
psbK=34770-34947\3;
psbL=34948-35076\3;
psbL=34949-35076\3;
psbL=34950-35076\3;
psbM=35077-35181\3;
psbM=35078-35181\3;
psbM=35079-35181\3;
psbN=35182-35313\3;
psbN=35183-35313\3;
psbN=35184-35313\3;
psbT=35314-35421\3;
psbT=35315-35421\3;
psbT=35316-35421\3;
rbcL=35422-36849\3;
rbcL=35423-36849\3;
rbcL=35424-36849\3;
rpl14=36850-37218\3;
rpl14=36851-37218\3;
rpl14=36852-37218\3;
rpl16=37219-37626\3;
rpl16=37220-37626\3;
rpl16=37221-37626\3;
rpl2=38029-38883\3;
rpl2=38030-38883\3;
rpl2=38031-38883\3;
rpl20=37627-38028\3;
rpl20=37628-38028\3;
rpl20=37629-38028\3;
rpl32=38884-39063\3;
rpl32=38885-39063\3;
rpl32=38886-39063\3;
rpl33=39064-39264\3;
rpl33=39065-39264\3;
rpl33=39066-39264\3;
rpl36=39265-39378\3;
rpl36=39266-39378\3;
rpl36=39267-39378\3;
rpoA=39379-40449\3;
rpoA=39380-40449\3;
rpoA=39381-40449\3;
rpoB=40450-43632\3;
rpoB=40451-43632\3;
rpoB=40452-43632\3;
rpoC1=43633-45690\3;
rpoC1=43634-45690\3;
rpoC1=43635-45690\3;
rpoC2=45691-49887\3;
rpoC2=45692-49887\3;
rpoC2=45693-49887\3;
rps11=49888-50304\3;
rps11=49889-50304\3;
rps11=49890-50304\3;
rps12=50305-50677\3;
rps12=50306-50677\3;
rps12=50307-50677\3;
rps14=50678-50980\3;
rps14=50679-50980\3;
rps14=50680-50980\3;
rps15=50981-51247\3;
rps15=50982-51247\3;
rps15=50983-51247\3;
rps16=51248-51517\3;
rps16=51249-51517\3;
rps16=51250-51517\3;
rps18=51518-51832\3;
rps18=51519-51832\3;
rps18=51520-51832\3;
rps19=51833-52111\3;
rps19=51834-52111\3;
rps19=51835-52111\3;
rps2=52112-52822\3;
rps2=52113-52822\3;
rps2=52114-52822\3;
rps3=52823-53485\3;
rps3=52824-53485\3;
rps3=52825-53485\3;
rps4=53486-54091\3;
rps4=53487-54091\3;
rps4=53488-54091\3;
rps7=54092-54559\3;
rps7=54093-54559\3;
rps7=54094-54559\3;
rps8=54560-54958\3;
rps8=54561-54958\3;
rps8=54562-54958\3;
ycf1=54959-60820\3;
ycf1=54960-60820\3;
ycf1=54961-60820\3;
ycf2=60821-68071\3;
ycf2=60822-68071\3;
ycf2=60823-68071\3;
ycf3=68072-68584\3;
ycf3=68073-68584\3;
ycf3=68074-68584\3;
ycf4=68585-69139\3;
ycf4=68586-69139\3;
ycf4=68587-69139\3;

[schemes]
search = rcluster;

--------------------------END------------------------