$ git clone --depth=50 --recursive --branch=staging git://github.com/greenelab/continuous_analysis_phylo.git /var/cache/drone/src/github.com/greenelab/continuous_analysis_phylo Cloning into '/var/cache/drone/src/github.com/greenelab/continuous_analysis_phylo'... $ git checkout -qf 9c9d07f2e9bbbedd5d3fe81c0f6c92acf48924d3 Output written to file "outfile"$ cd /var/cache/drone/src/github.com/greenelab/continuous_analysis_phylo/ $ mv data/twist.fasta twist.fasta $ rm -r dataTree also written onto file "outtree" $ mkdir data $ cd data Data set # 79:$ mv ../twist.fasta twist.fasta $ sh ../run_phylo.sh Adding species:nseq = 5 1. MouseTw2 distance = ktuples iterate = 0 cycle = 2 2. HumanTw1 nthread = 0 generating 200PAM scoring matrix for nucleotides ... done 3. MouseTw1 done done 4. FlyTw scoremtx = -1 Gap Penalty = -1.53, +0.00, +0.00 5. HumanTw2 tuplesize = 6, dorp = d Making a distance matrix .. Doing global rearrangements on all trees tied for best 1 / 5 !---------!done. .Constructing a UPGMA tree ... . 0 / 5. done.. . .Progressive alignment ... . STEP 1 / 4 f. STEP 2 / 4 f. STEP 3 / 4 f STEP 4 / 4 f .done. . .disttbfast (nuc) Version 7.123b alg=A, model=DNA200 (2), 1.530 ( 4.590), -0.000 (-0.000). 0 thread(s). .nthread = 0 .blosum 62 / kimura 200. .generating 200PAM scoring matrix for nucleotides ... done done doneCollapsing best trees scoremtx = -1 .Gap Penalty = -1.53, +0.00, +0.00 .Making a distance matrix .. . . 0 / 4. done.. . Constructing a UPGMA tree ... 0 / 5 .done. . .Progressive alignment ... . . STEP 1 /4 f STEP 2 /4 .f STEP 3 /4 .f STEP 4 /4 .f. done. tbfast (nuc) Version 7.123b alg=A, model=DNA200 (2), 1.530 ( 4.590), -0.000 (-0.000) 0 thread(s) Collapsing best trees . Strategy: FFT-NS-2 (Fast but rough) Progressive method (guide trees were built 2 times.) Output written to file "outfile" If unsure which option to use, try 'mafft --auto input > output'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. Tree also written onto file "outtree" The default gap scoring scheme has been changed in version 7.110 (2013 Oct). It tends to insert more gaps into gap-rich regions than previous versions. To disable this change, add the --legacygappenalty option.Data set # 84: Read and write (return) sequences Adding species: DNA parsimony algorithm, version 3.69 1. MouseTw2 Setting for this run: U Search for best tree? Yes S Search option? More thorough search 2. MouseTw1 V Number of trees to save? 10000 J Randomize input order of sequences? No. Use input order O Outgroup root? No, use as outgroup species 1 3. HumanTw2 T Use Threshold parsimony? No, use ordinary parsimony N Use Transversion parsimony? No, count all steps W Sites weighted? No 4. FlyTw M Analyze multiple data sets? No I Input sequences interleaved? Yes 0 Terminal type (IBM PC, ANSI, none)? ANSI 5. HumanTw1 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Print out steps in each site No 5 Print sequences at all nodes of tree NoDoing global rearrangements on all trees tied for best 6 Write out trees onto tree file? Yes !---------! Y to accept these or type the letter for one to change .Adding species: . 1. FlyTw . 2. HumanTw1 . . 3. MouseTw1 . 4. HumanTw2 . . 5. MouseTw2 . Doing global rearrangements on all trees tied for best !---------! . .............. . ........ ... Collapsing best treesCollapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree" Output written to file "outfile" Done. DRAWTREE from PHYLIP version 3.69 Tree also written onto file "outtree"Reading tree ... Tree has been read. Loading the font ... Font loaded. Data set # 85: Unrooted tree plotting program version 3.69 Here are the settings: Adding species: 0 Screen type (IBM PC, ANSI)? ANSI 1. MouseTw1 P Final plotting device: Postscript printer V Previewing device: X Windows display B Use branch lengths: Yes 2. HumanTw2 L Angle of labels: branch points to Middle of label R Rotation of tree: 90.0 I Iterate to improve tree: Equal-Daylight algorithm 3. MouseTw2 D Try to avoid label overlap? No S Scale of branch length: Automatically rescaled C Relative character height: 0.3333 4. FlyTw F Font: Times-Roman M Horizontal margins: 1.65 cm M Vertical margins: 2.16 cm 5. HumanTw1 # Page size submenu: one page per tree Y to accept these or type the letter for one to change  Which type of screen will it be previewed on?Doing global rearrangements on all trees tied for best type: to choose one compatible with: !---------! N will not be previewed . X X Windows display. K TeKtronix 4010 graphics terminal. D DEC ReGIS graphics (VT240 terminal). U other: one you have inserted code for. Choose one: . . . .  Unrooted tree plotting program version 3.69 . .Here are the settings: . . 0 Screen type (IBM PC, ANSI)? ANSI . P Final plotting device: Postscript printer . V Previewing device: (none) . B Use branch lengths: Yes . L Angle of labels: branch points to Middle of label . R Rotation of tree: 90.0 I Iterate to improve tree: Equal-Daylight algorithm D Try to avoid label overlap? No S Scale of branch length: Automatically rescaled Collapsing best trees C Relative character height: 0.3333 F Font: Times-Roman . M Horizontal margins: 1.65 cm M Vertical margins: 2.16 cm # Page size submenu: one page per tree Y to accept these or type the letter for one to change Output written to file "outfile" Writing plot file ... Plot written to file "plotfile"Tree also written onto file "outtree" Done. Data set # 86: Bootstrapping algorithm, version 3.69 Settings for this run:Adding species: D Sequence, Morph, Rest., Gene Freqs? Molecular sequences J Bootstrap, Jackknife, Permute, Rewrite? Bootstrap 1. HumanTw2 % Regular or altered sampling fraction? regular B Block size for block-bootstrapping? 1 (regular bootstrap) R How many replicates? 100 2. MouseTw2 W Read weights of characters? No C Read categories of sites? No S Write out data sets or just weights? Data sets 3. HumanTw1 I Input sequences interleaved? Yes 0 Terminal type (IBM PC, ANSI, none)? ANSI 1 Print out the data at start of run No 4. MouseTw1 2 Print indications of progress of run Yes Y to accept these or type the letter for one to change 5. FlyTw Random number seed (must be odd)? completed replicate number 10Doing global rearrangements on all trees tied for best completed replicate number 20 completed replicate number 30 !---------! completed replicate number 40 completed replicate number 50 . completed replicate number 60. completed replicate number 70. completed replicate number 80. completed replicate number 90. completed replicate number 100. . Output written to file "outfile". . Done. . .DNA parsimony algorithm, version 3.69 . .Setting for this run: . U Search for best tree? Yes . S Search option? More thorough search . V Number of trees to save? 10000 . J Randomize input order of sequences? No. Use input order . O Outgroup root? No, use as outgroup species 1 T Use Threshold parsimony? No, use ordinary parsimony N Use Transversion parsimony? No, count all steps W Sites weighted? No Collapsing best trees M Analyze multiple data sets? No I Input sequences interleaved? Yes . 0 Terminal type (IBM PC, ANSI, none)? ANSI 1 Print out the data at start of run No 2 Print indications of progress of run Yes 3 Print out tree Yes 4 Print out steps in each site No Output written to file "outfile" 5 Print sequences at all nodes of tree No 6 Write out trees onto tree file? Yes Y to accept these or type the letter for one to change Tree also written onto file "outtree"Multiple data sets or multiple weights? (type D or W) How many data sets? Random number seed (must be odd)?Data set # 87: Number of times to jumble?  DNA parsimony algorithm, version 3.69 Adding species: Setting for this run: U Search for best tree? Yes 1. HumanTw1 S Search option? More thorough search V Number of trees to save? 10000 J Randomize input order of sequences? Yes (seed = 55, 1 times) 2. FlyTw O Outgroup root? No, use as outgroup species 1 T Use Threshold parsimony? No, use ordinary parsimony N Use Transversion parsimony? No, count all steps 3. MouseTw1 W Sites weighted? No M Analyze multiple data sets? Yes, 100 data sets I Input sequences interleaved? Yes 4. HumanTw2 0 Terminal type (IBM PC, ANSI, none)? ANSI 1 Print out the data at start of run No 2 Print indications of progress of run Yes 5. MouseTw2 3 Print out tree Yes 4 Print out steps in each site No 5 Print sequences at all nodes of tree No 6 Write out trees onto tree file? Yes Doing global rearrangements on all trees tied for best Y to accept these or type the letter for one to change !---------! Data set # 1: . .Adding species: . 1. HumanTw2 . 2. MouseTw1 . . 3. HumanTw1 . 4. MouseTw2 . . 5. FlyTw Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 2: Adding species:Tree also written onto file "outtree" 1. MouseTw2 2. MouseTw1 3. HumanTw1 Data set # 88: 4. HumanTw2 5. FlyTw Adding species: Doing global rearrangements on all trees tied for best 1. MouseTw2 !---------! .... 2. FlyTw .. ... 3. HumanTw2 . .... 4. MouseTw1 .. .. 5. HumanTw1 Collapsing best trees .Collapsing best trees . Doing global rearrangements on all trees tied for best Output written to file "outfile" !---------! Tree also written onto file "outtree" . Data set # 5:. . Adding species:. 1. FlyTw . . 2. HumanTw1 . 3. MouseTw2 . . 4. HumanTw2 5. MouseTw1 . .Doing global rearrangements on all trees tied for best . !---------! . .............. . .... ..Collapsing best trees.. . Collapsing best trees . Output written to file "outfile" Output written to file "outfile" Tree also written onto file "outtree" Data set # 6: Tree also written onto file "outtree" Adding species: 1. MouseTw1 2. HumanTw1 Data set # 89: 3. HumanTw2 4. FlyTw Adding species: 5. MouseTw2 1. FlyTw Doing global rearrangements on all trees tied for best !---------! . 2. MouseTw2 .. .... 3. MouseTw1 .. .. 4. HumanTw2 .. .... 5. HumanTw1 . Collapsing best trees . Doing global rearrangements on all trees tied for bestOutput written to file "outfile" !---------!Tree also written onto file "outtree" .Data set # 7: . .Adding species: . 1. FlyTw . 2. HumanTw2 . . 3. MouseTw1 . 4. HumanTw1 . 5. MouseTw2 . Doing global rearrangements on all trees tied for best. !---------!. .............. . .. .... ..Collapsing best trees. .Collapsing best trees . Output written to file "outfile" Output written to file "outfile" Tree also written onto file "outtree" Data set # 8: Tree also written onto file "outtree" Adding species: 1. MouseTw2 2. HumanTw2 Data set # 90: 3. HumanTw1 4. FlyTw 5. MouseTw1 Adding species: 1. MouseTw1 Doing global rearrangements on all trees tied for best !---------! .. 2. HumanTw1 . Output written to file "outfile" 3. MouseTw2 Tree also written onto file "outtree" 4. FlyTw Data set # 3: Adding species: 5. HumanTw2 1. FlyTw 2. HumanTw2 3. MouseTw2 Doing global rearrangements on all trees tied for best 4. HumanTw1 5. MouseTw1 !---------! .Doing global rearrangements on all trees tied for best . !---------! . .............. ...... .. .... . Collapsing best trees. .. . .Output written to file "outfile" . .Tree also written onto file "outtree" Data set # 4: Collapsing best treesAdding species: 1. HumanTw1 . 2. HumanTw2 3. MouseTw1 4. MouseTw2 Output written to file "outfile" 5. FlyTw Doing global rearrangements on all trees tied for best !---------!Tree also written onto file "outtree" . .... ..Data set # 91:.. .. ..Adding species:.. .. 1. FlyTw . . 2. MouseTw1 .. ... 3. HumanTw2 . .... 4. MouseTw2 .. .. 5. HumanTw1 Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 9: . .Adding species: . 1. FlyTw . 2. MouseTw2 . . 3. HumanTw2 . 4. MouseTw1 . . 5. HumanTw1 Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 10: Adding species:Tree also written onto file "outtree" 1. FlyTw 2. HumanTw2 3. MouseTw2 Data set # 92: 4. HumanTw1 5. MouseTw1 Adding species: Doing global rearrangements on all trees tied for best 1. HumanTw1 !---------! .... 2. HumanTw2 .. ... 3. FlyTw . .... 4. MouseTw2 .. .. 5. MouseTw1 Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 11: . .Adding species: . 1. HumanTw1 . 2. FlyTw . . 3. MouseTw1 . 4. MouseTw2 . . 5. HumanTw2 Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 12: Adding species:Tree also written onto file "outtree" 1. MouseTw1 2. FlyTw 3. MouseTw2 Data set # 93: 4. HumanTw2 5. HumanTw1 Adding species: Doing global rearrangements on all trees tied for best 1. FlyTw !---------! .... 2. MouseTw1 .. ... 3. MouseTw2 . .... 4. HumanTw1 .. .. 5. HumanTw2 Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 13: . .Adding species: . 1. FlyTw . 2. HumanTw1 . . 3. HumanTw2 . 4. MouseTw1 . . 5. MouseTw2 Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 14: Adding species:Tree also written onto file "outtree" 1. FlyTw 2. MouseTw1 3. HumanTw2 Data set # 94: 4. HumanTw1 5. MouseTw2 Adding species: Doing global rearrangements on all trees tied for best 1. HumanTw1 !---------! .... 2. HumanTw2 .. ... 3. MouseTw2 . .... 4. MouseTw1 .. .. 5. FlyTw Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 15: . .Adding species: . 1. HumanTw1 . 2. MouseTw1 . . 3. MouseTw2 . 4. FlyTw . . 5. HumanTw2 Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 16: Adding species:Tree also written onto file "outtree" 1. MouseTw1 2. HumanTw2 3. MouseTw2 Data set # 95: 4. HumanTw1 5. FlyTw Adding species: Doing global rearrangements on all trees tied for best 1. FlyTw !---------! .... 2. HumanTw1 .. ... 3. MouseTw2 . .... 4. HumanTw2 .. .. 5. MouseTw1 Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 17: . .Adding species: . 1. HumanTw1 . 2. FlyTw . . 3. MouseTw2 . 4. MouseTw1 . . 5. HumanTw2 Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 18: Adding species:Tree also written onto file "outtree" 1. MouseTw2 2. HumanTw2 3. HumanTw1 Data set # 96: 4. MouseTw1 5. FlyTw Adding species: Doing global rearrangements on all trees tied for best 1. HumanTw1 !---------! .... 2. MouseTw2 .. ... 3. MouseTw1 . .... 4. FlyTw .. .. 5. HumanTw2 Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 19: . .Adding species: . 1. MouseTw1 . 2. FlyTw . . 3. MouseTw2 . 4. HumanTw2 . . 5. HumanTw1 Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 20: Adding species:Tree also written onto file "outtree" 1. MouseTw1 2. FlyTw 3. MouseTw2 Data set # 97: 4. HumanTw1 5. HumanTw2 Adding species: Doing global rearrangements on all trees tied for best 1. MouseTw1 !---------! .... 2. FlyTw .. ... 3. HumanTw2 . .... 4. HumanTw1 .. .. 5. MouseTw2 Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 21: . .Adding species: . 1. HumanTw1 . 2. MouseTw1 . . 3. FlyTw . 4. MouseTw2 . . 5. HumanTw2 Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . . Output written to file "outfile" Output written to file "outfile"Tree also written onto file "outtree" Data set # 23: Tree also written onto file "outtree"Adding species: 1. MouseTw2 2. HumanTw1 Data set # 98: 3. HumanTw2 4. MouseTw1 5. FlyTw Adding species: Doing global rearrangements on all trees tied for best 1. HumanTw2 !---------! ... 2. MouseTw1 .. .... 3. FlyTw .... 4. HumanTw1 .. ... 5. MouseTw2 Collapsing best trees . Output written to file "outfile"Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 24: . . Adding species:. 1. MouseTw2 . . 2. MouseTw1 . 3. HumanTw1 . . 4. HumanTw2 . 5. FlyTw .Doing global rearrangements on all trees tied for best . !---------! . .............. .... .... ..Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 25: Adding species:Tree also written onto file "outtree" 1. MouseTw2 2. HumanTw2 3. HumanTw1 Data set # 99: 4. MouseTw1 5. FlyTw Adding species: Doing global rearrangements on all trees tied for best 1. HumanTw1 !---------! .... 2. HumanTw2 .. ... 3. MouseTw1 . .... 4. FlyTw .. .. 5. MouseTw2 Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 26: . .Adding species: . 1. MouseTw2 . 2. MouseTw1 . . 3. HumanTw1 . 4. FlyTw . . 5. HumanTw2 Doing global rearrangements on all trees tied for best . !---------!. ........... . .Output written to file "outfile" . Tree also written onto file "outtree" Data set # 22: Collapsing best trees Adding species: . 1. FlyTw 2. HumanTw2 3. HumanTw1 4. MouseTw2 Output written to file "outfile" 5. MouseTw1 Doing global rearrangements on all trees tied for bestTree also written onto file "outtree" !---------! ... ..Data set # 100:.. .. ..Adding species:.. .. 1. HumanTw2 .. . 2. MouseTw1 Collapsing best trees Collapsing best trees.. 3. FlyTw . .... 4. HumanTw1 .. .. 5. MouseTw2 Collapsing best trees . Output written to file "outfile" Doing global rearrangements on all trees tied for best Tree also written onto file "outtree" !---------! Data set # 27: . .Adding species: . 1. HumanTw2 . 2. HumanTw1 . . 3. FlyTw . 4. MouseTw1 . . 5. MouseTw2 Doing global rearrangements on all trees tied for best . !---------!. .............. . ..... .... . Collapsing best trees Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree"Output written to file "outfile" Data set # 28: Adding species:Tree also written onto file "outtree" 1. HumanTw1 2. MouseTw2 3. FlyTw Done. 4. HumanTw2 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------!  .. ..Consensus tree program, version 3.69.. ... .Settings for this run:.. .. C Consensus type (MRe, strict, MR, Ml): Majority rule (extended).. .. O Outgroup root: No, use as outgroup species 1 Collapsing best trees R Trees to be treated as Rooted: No . T Terminal type (IBM PC, ANSI, none): ANSI Output written to file "outfile" 1 Print out the sets of species: Yes Tree also written onto file "outtree" 2 Print indications of progress of run: Yes Data set # 29: 3 Print out tree: Yes Adding species: 4 Write out trees onto tree file: Yes 1. HumanTw2 2. HumanTw1 3. FlyTw Are these settings correct? (type Y or the letter for one to change) 4. MouseTw2 5. MouseTw1 Doing global rearrangements on all trees tied for bestConsensus tree written to file "outtree" !---------! ... ..Output written to file "outfile".. .. ..Done... .... . $ convert plotfile tree.pngCollapsing best trees . $ cd .. Output written to file "outfile" Tree also written onto file "outtree"$ git config user.email "brettbj@gmail.com" Data set # 30: $ git config user.name "Brett Beaulieu-Jones" Adding species: 1. HumanTw1 $ git config --global push.default simple 2. MouseTw1 3. MouseTw2 $ git remote set-url origin https://github.com/greenelab/continuous_analysis_phylo.git 4. FlyTw 5. HumanTw2 $ git checkout -b master Doing global rearrangements on all trees tied for best !---------! Switched to a new branch 'master' .. ....M data/intree.. .M data/mafft.seq . ..M data/outfile.. ..M data/outtree.. M data/plotfile Collapsing best trees .M data/tree.png M data/twist-boot.alnOutput written to file "outfile" M data/twist-boot.outTree also written onto file "outtree" M data/twist.alnData set # 31: M data/twist.newickAdding species: 1. HumanTw2 M data/twist.tree 2. MouseTw1 3. HumanTw1 $ git add * 4. FlyTw 5. MouseTw2 $ git commit -a -m "Drone Build [skip ci] [ci skip]" Doing global rearrangements on all trees tied for best !---------![master 518fc9c] Drone Build [skip ci] [ci skip] . .. 11 files changed, 31540 insertions(+), 25403 deletions(-).. .. rewrite data/intree (100%).. rewrite data/mafft.seq (86%) .. .. rewrite data/tree.png (98%).. .. rewrite data/twist-boot.aln (67%). rewrite data/twist-boot.out (60%)Collapsing best trees . rewrite data/twist.aln (80%) Output written to file "outfile" rewrite data/twist.tree (60%) Tree also written onto file "outtree" $ git remote set-url origin https://brettbj:b84a2ed9aa01476fec202c914af56a614b5d7aeb@github.com/greenelab/continuous_analysis_phylo.git Data set # 32: Adding species:$ git push --set-upstream origin master 1. FlyTw 2. MouseTw1 3. HumanTw1 4. HumanTw2 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 33: Adding species: 1. HumanTw2 2. MouseTw1 3. HumanTw1 4. FlyTw 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 34: Adding species: 1. MouseTw1 2. FlyTw 3. HumanTw1 4. MouseTw2 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 35: Adding species: 1. FlyTw 2. HumanTw1 3. MouseTw2 4. HumanTw2 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 36: Adding species: 1. FlyTw 2. HumanTw1 3. MouseTw2 4. HumanTw2 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 37: Adding species: 1. MouseTw1 2. MouseTw2 3. FlyTw 4. HumanTw1 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 38: Adding species: 1. FlyTw 2. HumanTw1 3. MouseTw1 4. MouseTw2 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 39: Adding species: 1. MouseTw2 2. FlyTw 3. MouseTw1 4. HumanTw2 5. HumanTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 40: Adding species: 1. MouseTw1 2. HumanTw1 3. MouseTw2 4. FlyTw 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 44: Adding species: 1. FlyTw 2. HumanTw1 3. MouseTw2 4. HumanTw2 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 45: Adding species: 1. FlyTw 2. MouseTw2 3. HumanTw1 4. HumanTw2 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ..... ...... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 41: Adding species: 1. MouseTw2 . 2. HumanTw2 3. HumanTw1 4. FlyTw 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ........ Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 42: Adding species: 1. FlyTw 2. MouseTw1 3. HumanTw1 4. HumanTw2 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 43: Adding species: 1. HumanTw2 2. MouseTw2 3. MouseTw1 4. HumanTw1 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ............. Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 46: Adding species: 1. HumanTw1 2. HumanTw2 3. FlyTw 4. MouseTw2 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 47: Adding species: 1. MouseTw1 2. MouseTw2 3. HumanTw2 4. FlyTw 5. HumanTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 48: Adding species: 1. HumanTw1 2. FlyTw 3. MouseTw1 4. MouseTw2 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 49: Adding species: 1. FlyTw 2. HumanTw1 3. MouseTw1 4. HumanTw2 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 50: Adding species: 1. MouseTw1 2. MouseTw2 3. FlyTw 4. HumanTw1 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 51: Adding species: 1. MouseTw2 2. FlyTw 3. HumanTw2 4. HumanTw1 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 52: Adding species: 1. MouseTw2 2. MouseTw1 3. FlyTw 4. HumanTw2 5. HumanTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 53: Adding species: 1. HumanTw1 2. HumanTw2 3. MouseTw1 4. FlyTw 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 54: Adding species: 1. FlyTw 2. HumanTw2 3. MouseTw1 4. MouseTw2 5. HumanTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 55: Adding species: 1. MouseTw2 2. MouseTw1 3. HumanTw2 4. HumanTw1 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 56: Adding species: 1. MouseTw1 2. HumanTw1 3. HumanTw2 4. FlyTw 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 57: Adding species: 1. MouseTw2 2. FlyTw 3. MouseTw1 4. HumanTw1 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 58: Adding species: 1. HumanTw1 2. MouseTw2 3. MouseTw1 4. HumanTw2 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 59: Adding species: 1. MouseTw1 2. MouseTw2 3. HumanTw1 4. FlyTw 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 60: Adding species: 1. FlyTw 2. MouseTw1 3. HumanTw2 4. MouseTw2 5. HumanTw1 ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 64: Adding species: 1. MouseTw2 2. HumanTw2 3. MouseTw1 4. HumanTw1 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 65: Adding species: 1. FlyTw 2. HumanTw1 3. MouseTw1 4. HumanTw2 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees .. Doing global rearrangements on all trees tied for best !---------! ......... .......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 61: Adding species: 1. FlyTw 2. HumanTw2 3. HumanTw1 4. MouseTw1 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... . ...... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 62: Adding species: 1. HumanTw1 2. HumanTw2 3. MouseTw2 4. MouseTw1 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 63: Adding species: 1. HumanTw2 2. MouseTw1 3. HumanTw1 4. MouseTw2 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... Output written to file "outfile" Tree also written onto file "outtree" Data set # 66: Adding species: 1. HumanTw1 2. MouseTw2 3. FlyTw 4. HumanTw2 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 67: Adding species: 1. HumanTw1 2. FlyTw 3. MouseTw1 4. MouseTw2 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 68: Adding species: 1. HumanTw1 2. HumanTw2 3. MouseTw1 4. MouseTw2 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 69: Adding species: 1. FlyTw 2. MouseTw2 3. HumanTw2 4. HumanTw1 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 70: Adding species: 1. FlyTw 2. HumanTw2 3. MouseTw1 4. MouseTw2 5. HumanTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 71: Adding species: 1. MouseTw2 2. MouseTw1 3. HumanTw1 4. HumanTw2 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 72: Adding species: 1. HumanTw1 2. HumanTw2 3. FlyTw 4. MouseTw1 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 73: Adding species: 1. HumanTw1 2. MouseTw1 3. HumanTw2 4. MouseTw2 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 74: Adding species: 1. HumanTw2 2. MouseTw1 3. FlyTw 4. HumanTw1 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 75: Adding species: 1. MouseTw1 2. MouseTw2 3. HumanTw1 4. FlyTw 5. HumanTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 76: Adding species: 1. HumanTw1 2. FlyTw 3. HumanTw2 4. MouseTw1 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 77: Adding species: 1. MouseTw1 2. MouseTw2 3. HumanTw1 4. HumanTw2 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 78: Adding species: 1. FlyTw 2. HumanTw2 3. MouseTw1 4. MouseTw2 5. HumanTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . . Output written to file "outfile" Tree also written onto file "outtree" Data set # 80: Adding species: 1. HumanTw2 2. HumanTw1 3. MouseTw2 4. MouseTw1 5. FlyTw Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 81: Adding species: 1. MouseTw2 2. HumanTw2 3. FlyTw 4. HumanTw1 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 82: Adding species: 1. FlyTw 2. MouseTw1 3. HumanTw2 4. HumanTw1 5. MouseTw2 Doing global rearrangements on all trees tied for best !---------! ......... ......... Collapsing best trees . Output written to file "outfile" Tree also written onto file "outtree" Data set # 83: Adding species: 1. HumanTw1 2. HumanTw2 3. FlyTw 4. MouseTw2 5. MouseTw1 Doing global rearrangements on all trees tied for best !---------! ..To https://brettbj:b84a2ed9aa01476fec202c914af56a614b5d7aeb@github.com/greenelab/continuous_analysis_phylo.git 83a970e..518fc9c master -> master Branch master set up to track remote branch master from origin. $ exit 0