bio 1.2.1 → 1.3.0

data/test/data/blast/blastp-multi.m7

@@ -0,0 +1,188 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastp</BlastOutput_program>
+  <BlastOutput_version>blastp 2.2.18 [Mar-02-2008]</BlastOutput_version>
+  <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>BA000007.faa</BlastOutput_db>
+  <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID>
+  <BlastOutput_query-def>gi|1790845|gb|AAC77338.1| predicted DNA-binding transcriptional regulator [Escherichia coli str. K-12 substr. MG1655]</BlastOutput_query-def>
+  <BlastOutput_query-len>443</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>BLOSUM62</Parameters_matrix>
+      <Parameters_expect>0.001</Parameters_expect>
+      <Parameters_gap-open>11</Parameters_gap-open>
+      <Parameters_gap-extend>1</Parameters_gap-extend>
+      <Parameters_filter>F</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+  <BlastOutput_iterations>
+    <Iteration>
+      <Iteration_iter-num>2</Iteration_iter-num>
+      <Iteration_query-ID>lcl|2_0</Iteration_query-ID>
+      <Iteration_query-def>gi|1790846|gb|AAC77339.1| lipoate-protein ligase A [Escherichia coli str. K-12</Iteration_query-def>
+      <Iteration_query-len>346</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gi|13364823|dbj|BAB38768.1|</Hit_id>
+          <Hit_def>putative lipoate-protein ligase A [Escherichia coli O157:H7 str. Sakai]</Hit_def>
+          <Hit_accession>BAB38768</Hit_accession>
+          <Hit_len>562</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>697.197</Hsp_bit-score>
+              <Hsp_score>1798</Hsp_score>
+              <Hsp_evalue>0</Hsp_evalue>
+              <Hsp_query-from>9</Hsp_query-from>
+              <Hsp_query-to>346</Hsp_query-to>
+              <Hsp_hit-from>225</Hsp_hit-from>
+              <Hsp_hit-to>562</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>331</Hsp_identity>
+              <Hsp_positive>335</Hsp_positive>
+              <Hsp_align-len>338</Hsp_align-len>
+              <Hsp_qseq>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTVEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGITHEQVCEAITEAFFAHYGERVEAEIISPNKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFTWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPEQEKELRELSAWMAGAVR</Hsp_qseq>
+              <Hsp_hseq>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKTAEGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGIPHEQVCEAITEAFFAHYGERVEAEIISPDKTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERFSWGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFPDQEKELRELSTWIAGAVR</Hsp_hseq>
+              <Hsp_midline>MSTLRLLISDSYDPWFNLAVEECIFRQMPATQRVLFLWRNADTVVIGRAQNPWKECNTRRMEEDNVRLARRSSGGGAVFHDLGNTCFTFMAGKPEYDKTISTSIVLNALNALGVSAEASGRNDLVVKT EGDRKVSGSAYRETKDRGFHHGTLLLNADLSRLANYLNPDKKKLAAKGITSVRSRVTNLTELLPGI HEQVCEAITEAFFAHYGERVEAEIISP+KTPDLPNFAETFARQSSWEWNFGQAPAFSHLLDERF+WGGVELHFDVEKGHITRAQVFTDSLNPAPLEALAGRLQGCLYRADMLQQECEALLVDFP+QEKELRELS W+AGAVR</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>5361</Statistics_db-num>
+          <Statistics_db-len>1609188</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</Statistics_eff-space>
+          <Statistics_kappa>0.041</Statistics_kappa>
+          <Statistics_lambda>0.267</Statistics_lambda>
+          <Statistics_entropy>0.14</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+    </Iteration>
+    <Iteration>
+      <Iteration_iter-num>3</Iteration_iter-num>
+      <Iteration_query-ID>lcl|3_0</Iteration_query-ID>
+      <Iteration_query-def>gi|1790847|gb|AAC77340.1| conserved protein [Escherichia coli str. K-12 substr. MG1655]</Iteration_query-def>
+      <Iteration_query-len>214</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gi|13364823|dbj|BAB38768.1|</Hit_id>
+          <Hit_def>putative lipoate-protein ligase A [Escherichia coli O157:H7 str. Sakai]</Hit_def>
+          <Hit_accession>BAB38768</Hit_accession>
+          <Hit_len>562</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>432.95</Hsp_bit-score>
+              <Hsp_score>1112</Hsp_score>
+              <Hsp_evalue>7.66702e-123</Hsp_evalue>
+              <Hsp_query-from>1</Hsp_query-from>
+              <Hsp_query-to>214</Hsp_query-to>
+              <Hsp_hit-from>1</Hsp_hit-from>
+              <Hsp_hit-to>214</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>214</Hsp_identity>
+              <Hsp_positive>214</Hsp_positive>
+              <Hsp_align-len>214</Hsp_align-len>
+              <Hsp_qseq>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_qseq>
+              <Hsp_hseq>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_hseq>
+              <Hsp_midline>MARTKLKFRLHRAVIVLFCLALLVALMQGASWFSQNHQRQRNPQLEELARTLARQVTLNVAPLMRTDSPDEKRIQAILDQLTDESRILDAGVYDEQGDLIARSGESVEVRDRLALDGKKAGGYFNQQIVEPIAGKNGPLGYLRLTLDTHTLATEAQQVDNTTNILRLMLLLSLAIGVVLTRTLLQGKRTRWQQSPFLLTASKPVPEEEESEKKE</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>5361</Statistics_db-num>
+          <Statistics_db-len>1609188</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</Statistics_eff-space>
+          <Statistics_kappa>0.041</Statistics_kappa>
+          <Statistics_lambda>0.267</Statistics_lambda>
+          <Statistics_entropy>0.14</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+    </Iteration>
+    <Iteration>
+      <Iteration_iter-num>5</Iteration_iter-num>
+      <Iteration_query-ID>lcl|5_0</Iteration_query-ID>
+      <Iteration_query-def>gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]</Iteration_query-def>
+      <Iteration_query-len>322</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>gi|13364824|dbj|BAB38769.1|</Hit_id>
+          <Hit_def>3-phosphoserine phosphatase [Escherichia coli O157:H7 str. Sakai]</Hit_def>
+          <Hit_accession>BAB38769</Hit_accession>
+          <Hit_len>322</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>657.907</Hsp_bit-score>
+              <Hsp_score>1696</Hsp_score>
+              <Hsp_evalue>0</Hsp_evalue>
+              <Hsp_query-from>1</Hsp_query-from>
+              <Hsp_query-to>322</Hsp_query-to>
+              <Hsp_hit-from>1</Hsp_hit-from>
+              <Hsp_hit-to>322</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>322</Hsp_identity>
+              <Hsp_positive>322</Hsp_positive>
+              <Hsp_align-len>322</Hsp_align-len>
+              <Hsp_qseq>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_qseq>
+              <Hsp_hseq>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_hseq>
+              <Hsp_midline>MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLGAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSGSLNQK</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+        <Hit>
+          <Hit_num>2</Hit_num>
+          <Hit_id>gi|13363792|dbj|BAB37741.1|</Hit_id>
+          <Hit_def>zinc-transporting ATPase [Escherichia coli O157:H7 str. Sakai]</Hit_def>
+          <Hit_accession>BAB37741</Hit_accession>
+          <Hit_len>732</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>38.1206</Hsp_bit-score>
+              <Hsp_score>87</Hsp_score>
+              <Hsp_evalue>0.000899657</Hsp_evalue>
+              <Hsp_query-from>190</Hsp_query-from>
+              <Hsp_query-to>311</Hsp_query-to>
+              <Hsp_hit-from>569</Hsp_hit-from>
+              <Hsp_hit-to>668</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_hit-frame>1</Hsp_hit-frame>
+              <Hsp_identity>39</Hsp_identity>
+              <Hsp_positive>56</Hsp_positive>
+              <Hsp_gaps>24</Hsp_gaps>
+              <Hsp_align-len>123</Hsp_align-len>
+              <Hsp_qseq>VLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVN-EKAEVTIRHADLMGV</Hsp_qseq>
+              <Hsp_hseq>ISELNALGVKGVILTG----------DNPRAAAAIAGELGL---EFKAGLL-----PEDKVKAVTELNQHA--PLAM---VGDGINDAPAMKAAAIGIAMGSGTDVALETADAALTHNHLRGL</Hsp_hseq>
+              <Hsp_midline>+ +L  LG K  I +G          D  R  A +A EL +   +F   ++      + K K +T L Q    PLA    +GDG ND P +KAA +GIA  +   V  E A+  + H  L G+</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>5361</Statistics_db-num>
+          <Statistics_db-len>1609188</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</Statistics_eff-space>
+          <Statistics_kappa>0.041</Statistics_kappa>
+          <Statistics_lambda>0.267</Statistics_lambda>
+          <Statistics_entropy>0.14</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+    </Iteration>
+  </BlastOutput_iterations>
+</BlastOutput>

data/test/data/command/echoarg2.bat

@@ -0,0 +1 @@
+@echo %2

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