ngoto-bio 1.2.9.9001

data/test/data/genscan/sample.report

@@ -0,0 +1,63 @@
+GENSCAN 1.0	Date run: 30-May-103	Time: 14:06:28
+
+Sequence HUMRASH : 12942 bp : 68.17% C+G : Isochore 4 (57 - 100 C+G%)
+
+Parameter matrix: HumanIso.smat
+
+Predicted genes/exons:
+
+Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
+----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
+
+ 1.01 Init +   1664   1774  111  1  0   94   83   212 0.997  21.33
+ 1.02 Intr +   2042   2220  179  1  2  104   66   408 0.997  40.12
+ 1.03 Intr +   2374   2533  160  1  1   89   94   302 0.999  32.08
+ 1.04 Term +   3231   3350  120  2  0  115   48   202 0.980  18.31
+ 1.05 PlyA +   3722   3727    6                              -5.80
+
+ 2.00 Prom +   6469   6508   40                              -7.92
+ 2.01 Init +   8153   8263  111  1  0   94   83   212 0.998  21.33
+ 2.02 Intr +   8531   8709  179  1  2  104   66   408 0.997  40.12
+ 2.03 Intr +   8863   9022  160  1  1   89   94   302 0.999  32.08
+ 2.04 Term +   9720   9839  120  2  0  115   48   202 0.961  18.31
+
+Predicted peptide sequence(s):
+
+Predicted coding sequence(s):
+
+
+>HUMRASH|GENSCAN_predicted_peptide_1|189_aa
+MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
+QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
+AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
+CMSCKCVLS
+
+>HUMRASH|GENSCAN_predicted_CDS_1|570_bp
+atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
+atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
+cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
+caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
+gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
+aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
+gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
+tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
+cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
+tgcatgagctgcaagtgtgtgctctcctga
+
+>HUMRASH|GENSCAN_predicted_peptide_2|189_aa
+MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
+QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
+AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
+CMSCKCVLS
+
+>HUMRASH|GENSCAN_predicted_CDS_2|570_bp
+atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
+atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
+cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
+caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
+gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
+aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
+gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
+tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
+cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
+tgcatgagctgcaagtgtgtgctctcctga

data/test/data/iprscan/merged.raw

@@ -0,0 +1,32 @@
+Q9RHD9	D44DAE8C544CB7C1	267	HMMPfam	PF00575	S1	1	55	3.3E-6	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	HMMPfam	PF00575	S1	68	142	4.1E-19	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	HMMPfam	PF00575	S1	155	228	1.8E-19	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	S1	3	55	7.1E-7	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	S1	70	142	8.1E-20	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	HMMSmart	SM00316	S1	157	228	1.5E-21	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	ProfileScan	PS50126	S1	1	55	14.869	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	ProfileScan	PS50126	S1	72	142	20.809	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	ProfileScan	PS50126	S1	159	228	22.541	T	11-Nov-2005	IPR003029	RNA binding S1	Molecular Function:RNA binding (GO:0003723)
+Q9RHD9	D44DAE8C544CB7C1	267	FPrintScan	PR00681	RIBOSOMALS1	6	27	1.5E-17	T	11-Nov-2005	IPR000110	Ribosomal protein S1	Molecular Function:RNA binding (GO:0003723), Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
+Q9RHD9	D44DAE8C544CB7C1	267	FPrintScan	PR00681	RIBOSOMALS1	85	104	1.5E-17	T	11-Nov-2005	IPR000110	Ribosomal protein S1	Molecular Function:RNA binding (GO:0003723), Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
+Q9RHD9	D44DAE8C544CB7C1	267	FPrintScan	PR00681	RIBOSOMALS1	125	143	1.5E-17	T	11-Nov-2005	IPR000110	Ribosomal protein S1	Molecular Function:RNA binding (GO:0003723), Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
+Q9RHD9	D44DAE8C544CB7C1	267	superfamily	SSF50249	Nucleic_acid_OB	3	60	1.4E-7	T	11-Nov-2005	IPR008994	Nucleic acid-binding OB-fold	Molecular Function:nucleic acid binding (GO:0003676)
+Q9RHD9	D44DAE8C544CB7C1	267	superfamily	SSF50249	Nucleic_acid_OB	61	205	6.3999999999999995E-24	T	11-Nov-2005	IPR008994	Nucleic acid-binding OB-fold	Molecular Function:nucleic acid binding (GO:0003676)
+RS16_ECOLI	F94D07049A6D489D	82	HMMTigr	TIGR00002	S16	2	81	117.16	T	11-Nov-2005	IPR000307	Ribosomal protein S16	Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
+RS16_ECOLI	F94D07049A6D489D	82	superfamily	SSF54565	Ribosomal_S16	1	79	1.81E-8	T	11-Nov-2005	IPR000307	Ribosomal protein S16	Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
+RS16_ECOLI	F94D07049A6D489D	82	HMMPfam	PF00886	Ribosomal_S16	8	68	2.7000000000000004E-33	T	11-Nov-2005	IPR000307	Ribosomal protein S16	Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
+RS16_ECOLI	F94D07049A6D489D	82	BlastProDom	PD003791	Ribosomal_S16	10	77	4.0E-33	T	11-Nov-2005	IPR000307	Ribosomal protein S16	Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
+RS16_ECOLI	F94D07049A6D489D	82	ProfileScan	PS00732	RIBOSOMAL_S16	2	11	8.0E-5	T	11-Nov-2005	IPR000307	Ribosomal protein S16	Molecular Function:structural constituent of ribosome (GO:0003735), Cellular Component:intracellular (GO:0005622), Cellular Component:ribosome (GO:0005840), Biological Process:protein biosynthesis (GO:0006412)
+Y902_MYCTU	CD84A335CCFFE6D7	446	superfamily	SSF47384	His_kin_homodim	220	292	5.89E-7	T	11-Nov-2005	IPR009082	Histidine kinase, homodimeric	
+Y902_MYCTU	CD84A335CCFFE6D7	446	HMMSmart	SM00304	HAMP	170	222	1.8E-6	T	11-Nov-2005	IPR003660	Histidine kinase, HAMP region	Molecular Function:signal transducer activity (GO:0004871), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
+Y902_MYCTU	CD84A335CCFFE6D7	446	ProfileScan	PS50885	HAMP	170	222	7.777	T	11-Nov-2005	IPR003660	Histidine kinase, HAMP region	Molecular Function:signal transducer activity (GO:0004871), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
+Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF00672	HAMP	151	219	1.1E-8	T	11-Nov-2005	IPR003660	Histidine kinase, HAMP region	Molecular Function:signal transducer activity (GO:0004871), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
+Y902_MYCTU	CD84A335CCFFE6D7	446	ProfileScan	PS50109	HIS_KIN	237	446	34.449	T	11-Nov-2005	IPR005467	Histidine kinase	Biological Process:protein amino acid phosphorylation (GO:0006468), Molecular Function:kinase activity (GO:0016301)
+Y902_MYCTU	CD84A335CCFFE6D7	446	HMMSmart	SM00388	HisKA	230	296	1.4E-12	T	11-Nov-2005	IPR003661	Histidine kinase A, N-terminal	Molecular Function:two-component sensor molecule activity (GO:0000155), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
+Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF00512	HisKA	230	296	2.4E-11	T	11-Nov-2005	IPR003661	Histidine kinase A, N-terminal	Molecular Function:two-component sensor molecule activity (GO:0000155), Biological Process:signal transduction (GO:0007165), Cellular Component:membrane (GO:0016020)
+Y902_MYCTU	CD84A335CCFFE6D7	446	HMMSmart	SM00387	HATPase_c	338	446	2.9E-24	T	11-Nov-2005	IPR003594	ATP-binding region, ATPase-like	Molecular Function:ATP binding (GO:0005524)
+Y902_MYCTU	CD84A335CCFFE6D7	446	HMMPfam	PF02518	HATPase_c	338	445	2.5E-26	T	11-Nov-2005	IPR003594	ATP-binding region, ATPase-like	Molecular Function:ATP binding (GO:0005524)
+Y902_MYCTU	CD84A335CCFFE6D7	446	FPrintScan	PR00344	BCTRLSENSOR	374	388	2.0E-12	T	11-Nov-2005	IPR004358	Histidine kinase related protein, C-terminal	Biological Process:phosphorylation (GO:0016310), Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)
+Y902_MYCTU	CD84A335CCFFE6D7	446	FPrintScan	PR00344	BCTRLSENSOR	392	402	2.0E-12	T	11-Nov-2005	IPR004358	Histidine kinase related protein, C-terminal	Biological Process:phosphorylation (GO:0016310), Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)
+Y902_MYCTU	CD84A335CCFFE6D7	446	FPrintScan	PR00344	BCTRLSENSOR	406	424	2.0E-12	T	11-Nov-2005	IPR004358	Histidine kinase related protein, C-terminal	Biological Process:phosphorylation (GO:0016310), Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)
+Y902_MYCTU	CD84A335CCFFE6D7	446	FPrintScan	PR00344	BCTRLSENSOR	430	443	2.0E-12	T	11-Nov-2005	IPR004358	Histidine kinase related protein, C-terminal	Biological Process:phosphorylation (GO:0016310), Molecular Function:transferase activity, transferring phosphorus-containing groups (GO:0016772)

data/test/data/iprscan/merged.txt

@@ -0,0 +1,74 @@
+Sequence "Q9RHD9" crc64 checksum: D44DAE8C544CB7C1 length: 267 aa.
+
+InterPro       IPR000110      Ribosomal protein S1
+Molecular Function: RNA binding (GO:0003723), Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: ribosome (GO:0005840), Biological Process: protein biosynthesis (GO:0006412)
+method         AccNumber      shortName                               location
+FPrintScan     PR00681        RIBOSOMALS1                             T[6-27] 1.5e-17 T[85-104] 1.5e-17 T[125-143] 1.5e-17
+
+InterPro       IPR003029      RNA binding S1
+Molecular Function: RNA binding (GO:0003723)
+method         AccNumber      shortName                               location
+HMMPfam        PF00575        S1                                      T[1-55] 1.3e-08 T[68-142] 1.6e-21 T[155-228] 6.8e-22
+HMMSmart       SM00316        S1                                      T[3-55] 1.2e-06 T[70-142] 1.4e-19 T[157-228] 2.6e-21
+ProfileScan    PS50126        S1                                      T[1-55] 14.869 T[72-142] 20.809 T[159-228] 22.541
+
+InterPro       IPR008994      Nucleic acid-binding OB-fold
+method         AccNumber      shortName                               location
+superfamily    SSF50249       Nucleic acid-binding proteins           T[147-257] 2.5e-24 T[59-145] 2.4e-22 T[3-58] 9.2e-14
+
+InterPro       NULL           NULL
+method         AccNumber      shortName                               location
+Coil           coil           coiled-coil                             ?[225-246]
+Seg            seg            seg                                     ?[29-40] ?[84-98] ?[222-237]
+
+Sequence "RS16_ECOLI" crc64 checksum: F94D07049A6D489D length: 82 aa.
+
+InterPro       IPR000307      Ribosomal protein S16
+Molecular Function: structural constituent of ribosome (GO:0003735), Cellular Component: intracellular (GO:0005622), Cellular Component: ribosome (GO:0005840), Biological Process: protein biosynthesis (GO:0006412)
+method         AccNumber      shortName                               location
+BlastProDom    PD003791       sp_RS16_ECOLI_P02372;                   T[1-77] 3e-38
+HMMPfam        PF00886        Ribosomal_S16                           T[8-68] 1.1e-35
+HMMTigr        TIGR00002      S16                                     T[2-81] 8.8e-33
+ScanRegExp     PS00732        RIBOSOMAL_S16                           T[2-11] 8e-5
+superfamily    SSF54565       Ribosomal protein S16                   T[1-79] 9.4e-28
+
+Sequence "Y902_MYCTU" crc64 checksum: CD84A335CCFFE6D7 length: 446 aa.
+
+InterPro       IPR003594      ATP-binding region, ATPase-like
+Molecular Function: ATP binding (GO:0005524)
+method         AccNumber      shortName                               location
+HMMPfam        PF02518        HATPase_c                               T[338-445] 9.6e-29
+HMMSmart       SM00387        HATPase_c                               T[338-446] 5e-24
+
+InterPro       IPR003660      Histidine kinase, HAMP region
+Molecular Function: signal transducer activity (GO:0004871), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
+method         AccNumber      shortName                               location
+HMMPfam        PF00672        HAMP                                    T[151-219] 4.3e-11
+HMMSmart       SM00304        HAMP                                    T[170-222] 3.1e-06
+ProfileScan    PS50885        HAMP                                    T[170-222] 7.777
+
+InterPro       IPR003661      Histidine kinase A, N-terminal
+Molecular Function: two-component sensor molecule activity (GO:0000155), Biological Process: signal transduction (GO:0007165), Cellular Component: membrane (GO:0016020)
+method         AccNumber      shortName                               location
+HMMPfam        PF00512        HisKA                                   T[230-296] 9.2e-14
+HMMSmart       SM00388        HisKA                                   T[230-296] 2.4e-12
+
+InterPro       IPR004358      Bacterial sensor protein, C-terminal
+Molecular Function: two-component sensor molecule activity (GO:0000155), Biological Process: signal transduction (GO:0007165)
+method         AccNumber      shortName                               location
+FPrintScan     PR00344        BCTRLSENSOR                             T[374-388] 2e-12 T[392-402] 2e-12 T[406-424] 2e-12 T[430-443] 2e-12
+
+InterPro       IPR005467      Histidine kinase
+Biological Process: signal transduction (GO:0007165), Molecular Function: kinase activity (GO:0016301)
+method         AccNumber      shortName                               location
+ProfileScan    PS50109        HIS_KIN                                 T[237-446] 34.449
+
+InterPro       IPR009082      Histidine kinase, homodimeric
+method         AccNumber      shortName                               location
+superfamily    SSF47384       Homodimeric domain of signal transducing histidine kinase  T[220-292] 2.7e-11
+
+InterPro       NULL           NULL
+method         AccNumber      shortName                               location
+Seg            seg            seg                                     ?[44-55] ?[108-120] ?[160-173] ?[308-319] ?[400-424]
+superfamily    SSF55874       ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase  T[295-444] 4.6e-30
+

data/test/data/paml/codeml/control_file.txt

@@ -0,0 +1,30 @@
+seqfile = abglobin.aa
+treefile = abglobin.trees
+outfile = output.txt
+clock = 0
+ncatG = 8
+noisy = 0
+fix_omega = 0
+aaDist = 0
+fix_kappa = 1
+getSE = 0
+runmode = 0
+omega = 0.4
+aaRatefile = wag.dat
+method = 0
+seqtype = 2
+NSsites = 0
+fix_alpha = 0
+RateAncestor = 1
+verbose = 1
+icode = 0
+model = 1
+alpha = 0.5
+Small_Diff = 5.0e-06
+CodonFreq = 2
+cleandata = 1
+ndata = 1
+Mgene = 0
+kappa = 2
+Malpha = 0
+fix_blength = 0

data/test/data/paml/codeml/output.txt

@@ -0,0 +1,78 @@
+
+seed used = 552599837
+
+
+Data set 1
+      5    285
+
+human                            VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY RLTPEEKSAV TALWGKVNVD EVGGEALGRL LVVYPWTQRF FESFGDLSTP DAVMGNPKVK AHGKKVLGAF SDGLAHLDNL KGTFATLSEL HCDKLHVDPE NFRLLGNVLV CVLAHHFGKE FTPPVQAAYQ KVVAGVANAL AHKYH
+goat-cow                         VLSAADKSNV KAAWGKVGGN AGAYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGE KVAAALTKAV GHLDDLPGTL SDLSDLHAHK LRVDPVNFKL LSHSLLVTLA CHLPNDFTPA VHASLDKFLA NVSTVLTSKY RLTAEEKAAV TAFWGKVKVD EVGGEALGRL LVVYPWTQRF FESFGDLSTA DAVMNNPKVK AHGKKVLDSF SNGMKHLDDL KGTFAALSEL HCDKLHVDPE NFKLLGNVLV VVLARNFGKE FTPVLQADFQ KVVAGVANAL AHRYH
+rabbit                           VLSPADKTNI KTAWEKIGSH GGEYGAEAVE RMFLGFPTTK TYFPHFDFTH GSEQIKAHGK KVSEALTKAV GHLDDLPGAL STLSDLHAHK LRVDPVNFKL LSHCLLVTLA NHHPSEFTPA VHASLDKFLA NVSTVLTSKY RLSSEEKSAV TALWGKVNVE EVGGEALGRL LVVYPWTQRF FESFGDLSSA NAVMNNPKVK AHGKKVLAAF SEGLSHLDNL KGTFAKLSEL HCDKLHVDPE NFRLLGNVLV IVLSHHFGKE FTPQVQAAYQ KVVAGVANAL AHKYH
+rat                              VLSADDKTNI KNCWGKIGGH GGEYGEEALQ RMFAAFPTTK TYFSHIDVSP GSAQVKAHGK KVADALAKAA DHVEDLPGAL STLSDLHAHK LRVDPVNFKF LSHCLLVTLA CHHPGDFTPA MHASLDKFLA SVSTVLTSKY RLTDAEKAAV NALWGKVNPD DVGGEALGRL LVVYPWTQRY FDSFGDLSSA SAIMGNPKVK AHGKKVINAF NDGLKHLDNL KGTFAHLSEL HCDKLHVDPE NFRLLGNMIV IVLGHHLGKE FTPCAQAAFQ KVVAGVASAL AHKYH
+marsupial                        VLSDADKTHV KAIWGKVGGH AGAYAAEALA RTFLSFPTTK TYFPHFDLSP GSAQIQGHGK KVADALSQAV AHLDDLPGTM SKLSDLHAHK LRVDPVNFKL LSHCLIVTLA AHLSKDLTPE VHASMDKFFA SVATVLTSKY RLTSEEKNCI TTIWSKVQVD QTGGEALGRM LVVYPWTTRF FGSFGDLSSP GAVMSNSKVQ AHGAKVLTSF GEAVKHLDNL KGTYAKLSEL HCDKLHVDPE NFKMLGNIIV ICLAEHFGKD FTPECQVAWQ KLVAGVAHAL AHKYH
+
+
+
+Printing out site pattern counts
+
+
+         5        126  P
+
+human                            VLSPADKTNV AAWGGAHAEY GAEALERMFL SPTPHFLSHA QVKGKADTNV AVDMNALANL CLALPAEFAV LSSTPESAVT ALGNVDEVQF ETPDVMGKLG ASDLANFTCR VLCVAHFEPV AAYVNK
+goat-cow                         VLSAADKSNV AAWGGGNAAY GAEALERMFL SPTPHFLSHA QVKGEAATKV GLDLGTLDNL SLCLPNDFAV LNSTAEAAVT AFGKVDEVQF ETADVMNKLD SSNMKDFACK VLVVARFEVL ADFVNR
+rabbit                           VLSPADKTNI TAWEGSHGEY GAEAVERMFL GPTPHFFTHE QIKAKSETKV GLDLGALTNL CLNHPSEFAV LNSSSESAVT ALGNVEEVQF ESANVMNKLA ASELSNFKCR VLIVSHFEQV AAYVNK
+rat                              VLSADDKTNI NCWGGGHGEY GEEALQRMFA APTSHIVSPA QVKAKADAKA DVELGALTNF CLCHPGDFAM LSSTDAAAVN ALGNPDDVQY DSASIMGKIN ANDLKNFHCR MIIVGHLECA AAFVSK
+marsupial                        VLSDADKTHV AIWGGGHAAY AAEALARTFL SPTPHFLSPA QIQGKADSQV ALDLGTMKNL CIALSKDLEV FSATSENCIT TISQVDQTTF GSPGVMSALT SGEVKNYKCK IIICAEFDEC VAWLHK
+
+
+
+   16   21   10    1    1   10   17    1    1    2    1    1    3    1   13
+    1    2    1    1    5    2    1    5   15    1    1    5    1   10    1
+    1    7   10    1   14    1    1    1    1    1    3    1    2    1    1
+    1    1    1    1    1    1    1    1    1    1    1    4    1    4    1
+    1    1    1    1    2    1    1    1    1    1    1    1    1    1    1
+    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
+    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
+    1    1    1    1    1    1    1    1    1    1    1    1    1    1    1
+    1    1    1    1    1    1
+
+AAML (in paml version 4, June 2007)    ./test/material/codeml/abglobin.aa   Model: EqualInput dGamma (ncatG=8) ns =   5  ls = 285
+
+
+Frequencies..
+                                    A      R      N      D      C      Q      E      G      H      I      L      K      M      F      P      S      T      W      Y      V
+human                          0.1263 0.0211 0.0351 0.0526 0.0105 0.0140 0.0421 0.0702 0.0632 0.0000 0.1263 0.0772 0.0105 0.0526 0.0491 0.0561 0.0561 0.0105 0.0211 0.1053
+goat-cow                       0.1193 0.0246 0.0421 0.0632 0.0070 0.0140 0.0386 0.0737 0.0526 0.0000 0.1298 0.0842 0.0105 0.0596 0.0351 0.0596 0.0526 0.0105 0.0175 0.1053
+rabbit                         0.0982 0.0211 0.0421 0.0386 0.0070 0.0175 0.0596 0.0702 0.0667 0.0140 0.1228 0.0842 0.0070 0.0561 0.0386 0.0737 0.0561 0.0105 0.0211 0.0947
+rat                            0.1193 0.0211 0.0386 0.0667 0.0175 0.0175 0.0316 0.0807 0.0667 0.0246 0.1123 0.0842 0.0140 0.0491 0.0386 0.0596 0.0456 0.0105 0.0211 0.0807
+marsupial                      0.1088 0.0175 0.0211 0.0561 0.0175 0.0281 0.0351 0.0702 0.0632 0.0281 0.1088 0.0842 0.0175 0.0491 0.0351 0.0737 0.0667 0.0140 0.0211 0.0842
+
+Homogeneity statistic: X2 = 0.13569 G = 0.15654 
+
+Average                        0.114386 0.021053 0.035789 0.055439 0.011930 0.018246 0.041404 0.072982 0.062456 0.013333 0.120000 0.082807 0.011930 0.053333 0.039298 0.064561 0.055439 0.011228 0.020351 0.094035
+
+# constant sites:    170 (59.65%)
+ln Lmax (unconstrained) = -1189.106658
+
+
+TREE #  1:  (((3, 4), 1), 2, 5);   MP score: 177
+lnL(ntime:  7  np:  8):  -1817.465211     +0.000000
+   6..7     7..8     8..3     8..4     7..1     6..2     6..5  
+ 0.033639 0.038008 0.082889 0.187866 0.055050 0.096992 0.284574 0.588710
+
+tree length =   0.77902
+
+(((3: 0.082889, 4: 0.187866): 0.038008, 1: 0.055050): 0.033639, 2: 0.096992, 5: 0.284574);
+
+(((rabbit: 0.082889, rat: 0.187866): 0.038008, human: 0.055050): 0.033639, goat-cow: 0.096992, marsupial: 0.284574);
+
+Detailed output identifying parameters
+
+alpha (gamma, K = 8) =  0.58871
+rate:   0.01357  0.09006  0.22445  0.42476  0.71414  1.14510  1.85916  3.52875
+freq:   0.12500  0.12500  0.12500  0.12500  0.12500  0.12500  0.12500  0.12500
+
+Time used:  0:01
+
+
+Data set 2

data/test/data/paml/codeml/rates

@@ -0,0 +1,217 @@
+
+Estimated rates for sites from AAML.
+(((FYDL177C: 0.089767, PYDL177C: 0.044687): 0.021205, MYDL177C: 0.096521): 0.108719, BYDL177C: 0.058006);
+
+Frequencies and rates for categories (K=8)
+rate:  0.03346  0.14763  0.30690  0.51693  0.79689  1.18983  1.81043  3.19794
+freq:  0.12500  0.12500  0.12500  0.12500  0.12500  0.12500  0.12500  0.12500
+
+   Site  Freq   Data    Rate (posterior mean & category)
+
+      1     1  ***M    1.000     5
+      2     2  ***H    1.000     1
+      3     2  ***H    1.000     1
+      4     4  ***L    1.000     7
+      5     2  ***S    1.000     1
+      6     1  ***P    1.000     7
+      7     1  ***I    1.000     6
+      8     3  ***K    1.000     1
+      9     3  ***K    1.000     1
+     10     2  ***T    1.000     8
+     11     4  ***L    1.000     7
+     12     1  ***Y    1.000     8
+     13     3  ***K    1.000     1
+     14     1  ***A    1.000     7
+     15     4  ***L    1.000     7
+     16     1  ***D    1.000     2
+     17     1  ***R    1.000     8
+     18     1  ***N    1.000     1
+     19     1  ***Q    1.000     7
+     20     2  ***C    1.000     3
+     21     4  ***L    1.000     7
+     22     2  ***T    1.000     8
+     23     2  ***S    1.000     1
+     24     1  ***V    1.000     8
+     25     1  ***F    1.000     8
+     26     2  ***C    1.000     3
+     27     2  ***E    1.000     8
+     28     2  ***E    1.000     8
+     29     3  MMMM    0.638     1
+     30     1  SSSN    1.473     7
+     31    15  KKKK    0.645     1
+     32     6  NNNN    0.624     1
+     33     7  VVVV    0.709     1
+     34     8  GGGG    0.828     1
+     35     1  KRKK    1.510     7
+     36    13  LLLL    0.779     1
+     37     7  VVVV    0.709     1
+     38     1  KKKR    1.534     8
+     39     3  VIII    1.539     8
+     40     3  WWWW    0.861     1
+     41     6  NNNN    0.624     1
+     42     7  EEEE    0.654     1
+     43     7  SSSS    0.629     1
+     44     7  EEEE    0.654     1
+     45     7  VVVV    0.709     1
+     46    13  LLLL    0.779     1
+     47     2  VIVI    2.233     8
+     48     3  DDDD    0.662     1
+     49     8  RRRR    0.651     1
+     50    15  KKKK    0.645     1
+     51     7  SSSS    0.629     1
+     52    15  KKKK    0.645     1
+     53     3  FFFF    0.813     1
+     54     9  QQQQ    0.598     1
+     55     9  AAAA    0.681     1
+     56     8  RRRR    0.651     1
+     57     4  CCCC    0.845     1
+     58     4  CCCC    0.845     1
+     59     1  TTPT    1.553     8
+     60    13  LLLL    0.779     1
+     61     1  RQQQ    1.470     7
+     62     1  NDNN    1.472     7
+     63     9  QQQQ    0.598     1
+     64    15  KKKK    0.645     1
+     65     3  DDDD    0.662     1
+     66     4  IIII    0.671     1
+     67     1  SPPP    1.716     8
+     68     1  SFSF    2.387     8
+     69     3  VIII    1.539     8
+     70    13  LLLL    0.779     1
+     71     1  EQQQ    1.426     7
+     72     1  EDEE    1.509     7
+     73    13  LLLL    0.779     1
+     74     1  VVTT    1.653     8
+     75     9  QQQQ    0.598     1
+     76     2  SNNN    1.463     7
+     77     6  NNNN    0.624     1
+     78    15  KKKK    0.645     1
+     79     1  SASS    1.481     7
+     80     7  VVVV    0.709     1
+     81     7  SSSS    0.629     1
+     82    15  KKKK    0.645     1
+     83     9  AAAA    0.681     1
+     84     7  SSSS    0.629     1
+     85     4  HHHH    0.664     1
+     86     3  MMMM    0.638     1
+     87     4  HHHH    0.664     1
+     88     3  MMMM    0.638     1
+     89     2  YYYY    0.769     1
+     90     9  AAAA    0.681     1
+     91     3  WWWW    0.861     1
+     92     8  RRRR    0.651     1
+     93     5  TTTT    0.647     1
+     94     9  AAAA    0.681     1
+     95     7  EEEE    0.654     1
+     96     2  VIVI    2.233     8
+     97     1  PASS    2.257     8
+     98     2  SNNN    1.463     7
+     99     1  DEND    2.198     8
+    100     1  SLLL    1.779     8
+    101     1  NNHN    1.462     7
+    102     1  SFLF    2.403     8
+    103     9  QQQQ    0.598     1
+    104     1  H***    1.000     1
+    105     1  G***    1.000     1
+    106     2  N***    1.000     1
+    107     9  QQQQ    0.598     1
+    108     1  DDEE    1.646     8
+    109     9  QQQQ    0.598     1
+    110    15  KKKK    0.645     1
+    111    15  KKKK    0.645     1
+    112    15  KKKK    0.645     1
+    113     1  NSGS    2.221     8
+    114     1  GSNS    2.262     8
+    115    15  KKKK    0.645     1
+    116     1  NNAT    2.357     8
+    117     1  HNNN    1.475     7
+    118    15  KKKK    0.645     1
+    119     1  NKSS    2.237     8
+    120     2  NSNN    1.464     7
+    121     2  NSNN    1.464     7
+    122     1  NNSR    2.289     8
+    123     2  N***    1.000     1
+    124     4  HHHH    0.664     1
+    125     1  GAVA    2.305     8
+    126     1  NNND    1.485     7
+    127    15  KKKK    0.645     1
+    128     1  TSSS    1.476     7
+    129     1  TKRK    2.270     8
+    130     1  KMNK    2.247     8
+    131     1  IVIV    2.243     8
+    132     1  TITT    1.519     7
+    133     1  VVVM    1.621     8
+    134     9  QQQQ    0.598     1
+    135     2  PPPP    0.802     1
+    136    15  KKKK    0.645     1
+    137     6  NNNN    0.624     1
+    138     3  VIII    1.539     8
+    139     7  EEEE    0.654     1
+    140     9  QQQQ    0.598     1
+    141     8  GGGG    0.828     1
+    142     1  CSCC    1.771     8
+    143     9  AAAA    0.681     1
+    144     3  DDDD    0.662     1
+    145     4  CCCC    0.845     1
+    146     8  GGGG    0.828     1
+    147     7  EEEE    0.654     1
+    148     9  AAAA    0.681     1
+    149     1  AGGG    1.762     8
+    150     9  AAAA    0.681     1
+    151     8  GGGG    0.828     1
+    152     9  QQQQ    0.598     1
+    153     8  RRRR    0.651     1
+    154    13  LLLL    0.779     1
+    155    13  LLLL    0.779     1
+    156     5  TTTT    0.647     1
+    157    13  LLLL    0.779     1
+    158    13  LLLL    0.779     1
+    159     7  EEEE    0.654     1
+    160     8  RRRR    0.651     1
+    161     9  AAAA    0.681     1
+    162     6  NNNN    0.624     1
+    163     4  IIII    0.671     1
+    164     3  FFFF    0.813     1
+    165     6  NNNN    0.624     1
+    166     1  IVVV    1.581     8
+    167    13  LLLL    0.779     1
+    168     7  VVVV    0.709     1
+    169     4  IIII    0.671     1
+    170     7  VVVV    0.709     1
+    171     5  TTTT    0.647     1
+    172     8  RRRR    0.651     1
+    173     3  WWWW    0.861     1
+    174     2  YYYY    0.769     1
+    175     8  GGGG    0.828     1
+    176     8  GGGG    0.828     1
+    177     5  TTTT    0.647     1
+    178     2  PPPP    0.802     1
+    179    13  LLLL    0.779     1
+    180     8  GGGG    0.828     1
+    181     7  SSSS    0.629     1
+    182     7  SSSS    0.629     1
+    183     8  RRRR    0.651     1
+    184     3  FFFF    0.813     1
+    185     8  RRRR    0.651     1
+    186     4  HHHH    0.664     1
+    187     4  IIII    0.671     1
+    188     7  SSSS    0.629     1
+    189     5  TTTT    0.647     1
+    190     4  CCCC    0.845     1
+    191     9  AAAA    0.681     1
+    192     7  VVVV    0.709     1
+    193     7  EEEE    0.654     1
+    194     1  STTT    1.494     7
+    195    13  LLLL    0.779     1
+    196    15  KKKK    0.645     1
+    197    15  KKKK    0.645     1
+    198     8  GGGG    0.828     1
+    199     1  GGGE    1.784     8
+    200     1  FYFF    1.749     8
+    201    13  LLLL    0.779     1
+    202     1  PHPP    1.752     8
+
+lnL =   -907.674000
+
+mean(r^)=   1.0031  var(r^)=   0.2349
+Accuracy of rate prediction: corr(r^,r) =   0.4236