/*********************************************************************************/ /* PRALINE: A PROGRAM FOR MULTIPLE ALIGNMENT OF PROTEIN SEQUENCES */ /* */ /* copyright (c) 1998-2004 Jaap Heringa NIMR, London NW7 1AA, U.K. */ /* copyright (c) 2001-2004 Victor A. Simossis NIMR, London NW7 1AA, U.K. */ /* copyright (c) 2004- Jaap Heringa VU University, Amsterdam, NL */ /* copyright (c) 2004-2005 Victor A. Simossis VU University, Amsterdam, NL */ /* copyright (c) 2005-2009 Walter Pirovano VU University, Amsterdam, NL */ /* */ /* AUTHORS : Walter Pirovano, Victor A. Simossis, and Jaap Heringa */ /* ONLINE SERVER : http://www.ibi.vu.nl/programs/pralinewww */ /*********************************************************************************/ Set paths for webserver: Homedir /home/ibivu Expanded to /home/ibivu Expanded DATA_DIR from /data01/ibivu/data () Expanded APPS_DIR from /home/ibivu/apps (/home/ibivu) Expanded PRALINE_DIR from /home/ibivu/apps/praline-b (/home/ibivu/apps) Expanded BLAST_DIR from /home/ibivu/apps/blast (/home/ibivu/apps) Expanded PRED_DIR from /home/ibivu/tools (/home/ibivu) Expanded MAT_DIR from /home/ibivu/apps/praline-b/mat (/home/ibivu/apps/praline-b) When using PRALINE please cite: SECONDARY STRUCTURE INTEGRATION: Pirovano W., Simossis V.A. and Heringa J. (2009) submitted. TRANSMEMBRANE STRUCTURE INTEGRATION: Pirovano W., Feenstra K.A. and Heringa J. (2008) Bioinformatics 24(4), 492-497. HOMOLOGY-EXTENDED ALIGNMENT STRATEGY: Simossis V.A., Kleinjung J. and Heringa J. (2005) Nucleic Acids Res. 33(3), 812-824. ORIGINAL ALIGNMENT METHOD: Heringa J. (1999) Computers and Chemistry, 23, 341-364. SERVER USAGE: Simossis V.A. and Heringa J. (2003) Comp. Biol. Chem. 27(4-5), 511-519. Simossis V.A. and Heringa J. (2005) Nucleic Acids Res. 33, W289-W294. ...reading substitution values from file: /home/ibivu/apps/praline/mat/blosum62.mat The gap-open penalty is set to 15.00 The gap-extension penalty is set to 1.00 Option PSIDB is set ON with value: PSIDB=nr Option PSIHITS is set ON with value: 100 Option PSIITER is set ON with value: 3 Option PSIPREPRO is set ON with value: 0.010000 Option TMMAT is set ON with value: TMMAT=/home/ibivu/apps/praline/mat/phat75-73.mat Option T_GO is set ON with value: 16.500000 Option PHOBIUS is set ON Option TREE is set ON Option MSF is set ON ...reading transmembrane topology substitution values from file: /home/ibivu/apps/praline/mat/phat75-73.mat matrix: T Input file msl_ref7.fasta contains 14 sequences 1. MSCL_ECOLI MSIIKEFREFAMRGNVVDLAVGVIIGAAFGKIVSSLVADIIMPPLGLLIGGIDFKQFAVTLRDAQGDIPAVVMHYGVFIQNVFDFLIVAFAIFMAIKLIN KLNRKKEEPAAAPAPTKEEVLLTEIRDLLKEQNNRS 136 amino acids 2. MSCL_ERWCA MSIIKEFREFAMRGNVVDLAVGVIIGALFGKIVSSLVSDIIMPPLGLLIGGVDFKQFALFLRNAQGGIPAVVMNYGAFIQNIFDFIIVAFAIFIAIKLMN KMRCKQEDTPAAPPKPSAEEKLLAEIRDLLKEQQTRQ 137 amino acids 3. MSCL_HAEIN MNFIKEFREFAMRGNVVDMAVGVIIGSAFGKIVSSLVSDIFTPVLGILTGGIDFKDMKFVLAQAQGDVPAVTLNYGLFIQNVIDFIIIAFAIFMMIKVIN KVRKPEEKKTAPKAETLLTEIRDLLKNK 128 amino acids 4. MSCL_PSEFL MGLLSEFKAFAVKGNVVDMAVGIIIGAAFGKIVSSFVGDVIMPPIGLLIGGVDFSDLAITLKAEGDVPAVVLAYRKFIQTVLNFVIVAFAIFMGVKAINR LKREEAVAPSEPPVPSAEETLLTEIRDLLKAQQNKS 136 amino acids 5. MSCL_Q9RH75 MSGVDEKGRRMLKEFREFAMKGNVVDLAVGVIIRRAFGAIVTSLVGDVIMPLIGAVTGGLDFSNYFTPLSKAVTATNLADAKKQGAVLAWGSFLTLTINF IIIAFVLFLVIRAINTLKRKEEAAPAAPPKPSAEVELLTEIRDLLKKSCTRTLRPNC 157 amino acids 6. MSCL_BACSU MWNEFKAFAMRGNIVDLAIGVVIGGAFGKIVTSLVNDIIMPLVGLLLGGLDFSGLSFTFGDAVVKYGSFIQTIVNFLIISFSIFIVIRTLNGLRRKKEAE EEAAEEAVDAQEELLKEIRDLLKQQAKSPE 130 amino acids 7. MSCL_CLOPE MWKEFKEFAMKGNVIDLAIGVVIGGAFGKIVTSLVNDIIMPVVGSLVGKVDFSNLYINLSGQQFNSLQEAQAAGAATINYGLFLNNLINFLIIAFSIFIV IKQINKLKNFTKKKEEVKVEATEKDCPYCYTKIDIKATRCPHCTSVLEEATN 152 amino acids 8. MSCL_CLOHI MWKDFKEFAMKGNVVDLAVGVIIGGAFGKIVTSLVNDVIMPILGLILGGINFTSAKLTLHGLNSEKPLTLNYGQFIQNILDFLIISFSIFLFIRLINRFK RKEEAVEEAKIPEISREEELLGEIRDLLKEKNK 133 amino acids 9. MSCL_SYNY3 MVKSARQGAGGFWRDFKDFILRGNVVDLAVAVVIGGAFTSIVNAFVAWLMAVLLQPVLDQAGVSQLQDLPLGLGELVIAIINFLIIAFVIFLIIKAIEKM QRKKAVEEEIVAEAQPDPVLEAQTNLTDSINRLITTLENQQSSSQ 145 amino acids 10. MSCL_STAAU MLKEFKEFALKGNVLDLAIAVVMGAAFNKIISSLVENIIMPLIGKIFGSVDFAKEWSFWGIKYGLFIQSVIDFIIIAFALFIFVKIANTLMKKEEAEEEA VVEENVVLLTEIRDLLREKK 120 amino acids 11. MSCL_MYCTU MLKGFKEFLARGNIVDLAVAVVIGTAFTALVTKFTDSIITPLINRIGVNAQSDVGILRIGIGGGQTIDLNVLLSAAINFFLIAFAVYFLVVLPYNTLRKK GEVEQPGDTQVVLLTEIRDLLAQTNGDSPGRHGGRGTPSPTDGPRASTESQ 151 amino acids 12. 1msla ARGNIVDLAVAVVIGTAFTALVTKFTDSIITPLINRIGVNAQSDVGILRIGIGGGQTIDLNVLLSAAINFFLIAFAVYFLVVLPYNTLRKKGEVEQPGDT QVVLLTEIR 109 amino acids 13. MSCL_MYCLE MFRGFKEFLSRGNIVDLAVAVVIGTAFTALITKFTDSIITPLINRVGVNQQTNISPLRIDIGGDQAIDLNIVLSAAINFLLIALVVYFLVVLPYTTIRKH GEVEQFDTDLIGNQVVLLAEIRDLLAQSNGAPSGRHVDTADLTPTPNHEPRADT 154 amino acids 14. MSCL_Q9RRR4 MLNGFRDFILRGNVVDLAVGVVIGAAFNNVVAAFTKAFLDPLIRLATGGHGKVAGTFAVNGITFDWGTFVSTLINFLLTAAVLYFFVVMPMNAATERLKR SEKAAEAEPSNEEKLLAEIRDAVRSRPL 128 amino acids Running PSI-BLAST (e-value threshold: 0.010000) for sequence [1] MSCL_ECOLI Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_ECOLI-msl_ref7_psiali.fasta Removed 13 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_ECOLI Running PSI-BLAST (e-value threshold: 0.010000) for sequence [2] MSCL_ERWCA Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_ERWCA-msl_ref7_psiali.fasta Removed 11 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_ERWCA Running PSI-BLAST (e-value threshold: 0.010000) for sequence [3] MSCL_HAEIN Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_HAEIN-msl_ref7_psiali.fasta Removed 17 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_HAEIN Running PSI-BLAST (e-value threshold: 0.010000) for sequence [4] MSCL_PSEFL Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_PSEFL-msl_ref7_psiali.fasta Removed 15 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_PSEFL Running PSI-BLAST (e-value threshold: 0.010000) for sequence [5] MSCL_Q9RH75 Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_Q9RH75-msl_ref7_psiali.fasta Removed 7 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_Q9RH75 Running PSI-BLAST (e-value threshold: 0.010000) for sequence [6] MSCL_BACSU Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_BACSU-msl_ref7_psiali.fasta Removed 12 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_BACSU Running PSI-BLAST (e-value threshold: 0.010000) for sequence [7] MSCL_CLOPE Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_CLOPE-msl_ref7_psiali.fasta Removed 9 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_CLOPE Running PSI-BLAST (e-value threshold: 0.010000) for sequence [8] MSCL_CLOHI Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_CLOHI-msl_ref7_psiali.fasta Removed 18 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_CLOHI Running PSI-BLAST (e-value threshold: 0.010000) for sequence [9] MSCL_SYNY3 Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_SYNY3-msl_ref7_psiali.fasta Removed 3 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_SYNY3 Running PSI-BLAST (e-value threshold: 0.010000) for sequence [10] MSCL_STAAU Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_STAAU-msl_ref7_psiali.fasta Removed 18 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_STAAU Running PSI-BLAST (e-value threshold: 0.010000) for sequence [11] MSCL_MYCTU Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_MYCTU-msl_ref7_psiali.fasta Removed 14 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_MYCTU Running PSI-BLAST (e-value threshold: 0.010000) for sequence [12] 1msla Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/1msla-msl_ref7_psiali.fasta Removed 26 redundant sequences from 101 hits. Running POLY-PHOBIUS on 1msla Running PSI-BLAST (e-value threshold: 0.010000) for sequence [13] MSCL_MYCLE Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_MYCLE-msl_ref7_psiali.fasta Removed 12 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_MYCLE Running PSI-BLAST (e-value threshold: 0.010000) for sequence [14] MSCL_Q9RRR4 Filtering PSI-BLAST alignment file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/MSCL_Q9RRR4-msl_ref7_psiali.fasta Removed 12 redundant sequences from 101 hits. Running POLY-PHOBIUS on MSCL_Q9RRR4 [0s] MSCL_ECOLI #---------MSIIKEFREFAMRGNVVDLAVGVIIGAAFGKIVSSLVADII [0tmp] # ttttttttttttttttttttttttttt [0s] MSCL_ERWCA #---------MSIIKEFREFAMRGNVVDLAVGVIIGALFGKIVSSLVSDII [0tmp] # tttttttttttttttttttttttttt [0s] MSCL_PSEFL #---------MGLLSEFKAFAVKGNVVDMAVGIIIGAAFGKIVSSFVGDVI [0tmp] # ttttttttttttttttttttttttttt [0s] MSCL_CLOHI #-----------MWKDFKEFAMKGNVVDLAVGVIIGGAFGKIVTSLVNDVI [0tmp] # ttttttttttttttttttttttttttt [0s] MSCL_BACSU #-----------MWNEFKAFAMRGNIVDLAIGVVIGGAFGKIVTSLVNDII [0tmp] # ttttttttttttttttttttttttttt [0s] MSCL_Q9RH75 #-MSGVDEKGRRMLKEFREFAMKGNVVDLAVGVIIRRAFGAIVTSLVGDVI [0tmp] # ttttttttttttttttttttttt [0s] MSCL_HAEIN #---------MNFIKEFREFAMRGNVVDMAVGVIIGSAFGKIVSSLVSDIF [0tmp] # ttttttttttttttttttttttt [0s] MSCL_SYNY3 #MVKSARQGAGGFWRDFKDFILRGNVVDLAVAVVIGGAFTSIVNAFVAWLM [0tmp] # ttttttttttttttttttttttttt [0s] MSCL_Q9RRR4 #-----------MLNGFRDFILRGNVVDLAVGVVIGAAFNNVVAAFTKAFL [0tmp] # tttttttttttttttttttttttttttt [0s] MSCL_CLOPE #-----------MWKEFKEFAMKGNVIDLAIGVVIGGAFGKIVTSLVNDII [0tmp] # ttttttttttttttttttttttt [0s] MSCL_MYCTU #-----------MLKGFKEFLARGNIVDLAVAVVIGTAFTALVTKFTDSII [0tmp] # tttttttttttttttttttttttt [0s] MSCL_MYCLE #-----------MFRGFKEFLSRGNIVDLAVAVVIGTAFTALITKFTDSII [0tmp] # tttttttttttttttttttttttt [0s] MSCL_STAAU #-----------MLKEFKEFALKGNVLDLAIAVVMGAAFNKIISSLVENII [0tmp] # tttttttttttttttttttttttt [0s] 1msla #--------------------ARGNIVDLAVAVVIGTAFTALVTKFTDSII [0tmp] # ttttttttttttttttttttttt [0c] Conservation #0000000000064658768568**99*9*97999859*568977774588 [0s] MSCL_ECOLI #MPPLGLLIGGIDFKQFAVTLRD-------AQGDIPAVVMHYGVFIQNVFD [0tmp] #ttttt tttttttttt [0s] MSCL_ERWCA #MPPLGLLIGGVDFKQFALFLRN-------AQGGIPAVVMNYGAFIQNIFD [0tmp] #tttttt ttttttttttt [0s] MSCL_PSEFL #MPPIGLLIGGVDFSDLAITLKA-------E-GDVPAVVLAYRKFIQTVLN [0tmp] #ttttttt ttttttttttt [0s] MSCL_CLOHI #MPILGLILGGINFTSAKLTLHG-------LNSEKP-LTLNYGQFIQNILD [0tmp] #ttttttt ttttttttttt [0s] MSCL_BACSU #MPLVGLLLGGLDFSGLSFTFGD-------A-------VVKYGSFIQTIVN [0tmp] #ttttttt tttttttttt [0s] MSCL_Q9RH75 #MPLIGAVTGGLDFSNYFTPLSKAVTATNLADAKKQGAVLAWGSFLTLTIN [0tmp] # tttttttttttt [0s] MSCL_HAEIN #TPVLGILTGGIDFKDMKFVLAQ-------AQGDVPAVTLNYGLFIQNVID [0tmp] # tttttttttt [0s] MSCL_SYNY3 #AVLLQPVLDQAGVSQL------------------QDLPLGLGELVIAIIN [0tmp] # ttttttttttt [0s] MSCL_Q9RRR4 #DPLIRLATGGHGKVAGTFAV--------------NGITFDWGTFVSTLIN [0tmp] #tttttt tttttttttt [0s] MSCL_CLOPE #MPVVGSLVGKVDFSNLYINLSGQQFNSLQEAQAAGAATINYGLFLNNLIN [0tmp] # ttttttttttt [0s] MSCL_MYCTU #TPLINRI--GVNAQSDVGILRI---------GIGGGQTIDLNVLLSAAIN [0tmp] # tttttttttt [0s] MSCL_MYCLE #TPLINRV--GVNQQTNISPLRI---------DIGGDQAIDLNIVLSAAIN [0tmp] # tttttttttt [0s] MSCL_STAAU #MPLIGKIFGSVDFAKEW-----------------SFWGIKYGLFIQSVID [0tmp] # ttttttttttt [0s] 1msla #TPLINRI--GVNAQSDVGILRI---------GIGGGQTIDLNVLLSAAIN [0tmp] #tttt tttttttttt [0c] Conservation #58586473576655433226310000000102113335745647855677 [0s] MSCL_ECOLI #FLIVAFAIFMAI-KLINKLNRKKE-EPAA-APAPT-----KEEVLLTEIR [0tmp] #tttttttttttt [0s] MSCL_ERWCA #FIIVAFAIFIAI-KLMNKMRCKQEDTPAA-PPKPS-----AEEKLLAEIR [0tmp] #tttttttttttt [0s] MSCL_PSEFL #FVIVAFAIFMGV-KAINRLKREEAVAPSE-PPVPS-----AEETLLTEIR [0tmp] #tttttttttttt [0s] MSCL_CLOHI #FLIISFSIFLFI-RLINRFKRKEEAVEEAKIPEIS-----REEELLGEIR [0tmp] #tttttttttttt [0s] MSCL_BACSU #FLIISFSIFIVI-RTLNGLRRKKEAEEEAAEEAVD-----AQEELLKEIR [0tmp] #tttttttttttt [0s] MSCL_Q9RH75 #FIIIAFVLFLVI-RAINTLKRKEEAAPAA-PPKPS-----AEVELLTEIR [0tmp] #tttttttttttt [0s] MSCL_HAEIN #FIIIAFAIFMMI-KVINKVRKPEE------KKTAP-----KAETLLTEIR [0tmp] #tttttttttttt [0s] MSCL_SYNY3 #FLIIAFVIFLII-KAIEKMQRKKAVEEEIVAEAQPDPVLEAQTNLTDSIN [0tmp] #tttttttttttt [0s] MSCL_Q9RRR4 #FLLTAAVLYFFVVMPMNAATERLKRSEKAAEAEPS-----NEEKLLAEIR [0tmp] #ttttttttttttt [0s] MSCL_CLOPE #FLIIAFSIFIVI-KQINKLKNFTKKKEEVKVEATE-----KDCPYCYTKI [0tmp] #tttttttttttt [0s] MSCL_MYCTU #FFLIAFAVYFLVVLPYNTLRKKGEV----EQPGD------TQVVLLTEIR [0tmp] #ttttttttttttt [0s] MSCL_MYCLE #FLLIALVVYFLVVLPYTTIRKHGEVEQFDTDLIG------NQVVLLAEIR [0tmp] #ttttttttttttt [0s] MSCL_STAAU #FIIIAFALFIFV-KIANTLMKKEEAEEEAVVE--------ENVVLLTEIR [0tmp] #tttttttttttt [0s] 1msla #FFLIAFAVYFLVVLPYNTLRKKGEVEQPGD----------TQVVLLTEIR [0tmp] #ttttttttttttt [0c] Conservation #*7889868864905458576664733434134322000004654985887 [0s] MSCL_ECOLI #DLLKEQNNRS------------------------- [0tmp] # [0s] MSCL_ERWCA #DLLKEQQTRQ------------------------- [0tmp] # [0s] MSCL_PSEFL #DLLKAQQNKS------------------------- [0tmp] # [0s] MSCL_CLOHI #DLLKEKNK--------------------------- [0tmp] # [0s] MSCL_BACSU #DLLKQQAKSPE------------------------ [0tmp] # [0s] MSCL_Q9RH75 #DLLKKSCTRTLRPNC-------------------- [0tmp] # [0s] MSCL_HAEIN #DLLKNK----------------------------- [0tmp] # [0s] MSCL_SYNY3 #RLITTLENQQSSSQ--------------------- [0tmp] # [0s] MSCL_Q9RRR4 #DAVRSRPL--------------------------- [0tmp] # [0s] MSCL_CLOPE #DIKATRCPHCTSVLEEATN---------------- [0tmp] # [0s] MSCL_MYCTU #DLLAQTNGDSPGRHGGRG--TPSPTDGPRASTESQ [0tmp] # [0s] MSCL_MYCLE #DLLAQSNGAPSGRHVDTADLTPTPNHEPRADT--- [0tmp] # [0s] MSCL_STAAU #DLLREKK---------------------------- [0tmp] # [0s] 1msla #----------------------------------- [0tmp] # [0c] Conservation #77654422110000000000000000000000000 Iteration 0 SP= 136062.00 AvSP= 12.071 SId= 4822 AvSId= 0.428 Nseq= 14 Len= 185 Naa= 1916 Ngaps= 674 [tr0] --------- 1 MSCL_ECOLI [tr0] --------------+ 2235.7 [tr0] | |-------- 2 MSCL_ERWCA [tr0] | -+ 2241.1 [tr0] | -------- 4 MSCL_PSEFL [tr0] ------+ 2152.8 [tr0] | ----------------------- 8 MSCL_CLOHI [tr0] ----+ 2111.4 [tr0] | ----------------------------- 6 MSCL_BACSU [tr0] ---------+ 2088.9 [tr0] | --------------------------------- 5 MSCL_Q9RH75 [tr0] -----+ 2030.8 [tr0] | ------------------------------------------ 3 MSCL_HAEIN [tr0] ------+ 1999.5 [tr0] | ----------------------------------------------- 9 MSCL_SYNY3 [tr0] ------+ 1962.3 [tr0] | ----------------------------------------------------- 14 MSCL_Q9RRR4 [tr0] ---+ 1924.4 [tr0] | ----------------------------------------------------------- 7 MSCL_CLOPE [tr0] --------+ 1910.4 [tr0] | | -------------------------- 11 MSCL_MYCTU [tr0] | ------------------------------------+ 2132.7 [tr0] | -------------------------- 13 MSCL_MYCLE [tr0]--------------------------------------+ 1855.2 [tr0]| ---------------------------------------------------------------------- 10 MSCL_STAAU [tr0]+ 1617.0 [tr0]------------------------------------------------------------------------------------------------------------ 12 1msla Alignment written to file /data01/scratch/jobs/ba4b9d337bea338b18b0f57d934e60c8/msl_ref7.msf PRALINE computation time has been: 1600.000 seconds (26 mins 40 secs) Command line used: /home/ibivu/apps/praline-b/praline msl_ref7.fasta /home/ibivu/apps/praline/mat/blosum62.mat 15 1 psidb=nr psihits=100 psiiter=3 psiprepro=0.010000 tmmat=/home/ibivu/apps/praline/mat/phat75-73.mat T_GO=16.500000 phobius tree msf 1> results.out 2> errors.out