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Cymon working#6

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cymon wants to merge 88 commits intopgfoster:masterpgfoster/p4-phylogenetics:masterfrom cymon:cymon-workingcymon/p4-phylogenetics:cymon-workingCopy head branch name to clipboard

+417-45

Commits

Commits on Nov 18, 2016

• Initial configuration

  cymon

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  b8be055

• mcmc.writeProposalProbs can now return a dictionary of proposal:values

  cymon

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  2064d66

• Added vim .swp to gitignore

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  a83025f

Commits on Nov 25, 2016

• Merge branch 'master' into cymon-working

  cymon

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  501e56b

Commits on Nov 29, 2016

• func.summariseMcmcPrams can now return a dictionary with makeDict argument

  cymon

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  7083997

Commits on Nov 30, 2016

• Changed gsl search paths in setup.py

  cymon

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  82a3e04

Commits on Dec 23, 2016

• Merge branch 'master' into cymon-working

  cymon

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  13adc1b

• Merge branch 'master' into cymon-working

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  2c406d9

Commits on Jan 2, 2017

• Fixed makeDict in writeProposalProbs() to deal with multiple partitions and CVs

  cymon

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  16b494d

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

  cymon

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  e79571d

Commits on Jan 16, 2017

• Merge branch 'master' into cymon-working

  cymon

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  ab16187

Commits on Jan 18, 2017

• Added new GSL package library paths for Ubuntu 16.04 and greater. Fixed

  Show description for 766e6e3
  cymon

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  766e6e3

Commits on Feb 7, 2017

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

  cymon

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  0a4ff21

Commits on Mar 7, 2017

• Return all stats from tail-area prob test. Add offset to writePhylip()

  Show description for 8e8800e
  cymon

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  8e8800e

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

  Show description for 5362b28
  cymon

  committed
  5362b28

• Fixed print statement

  cymon

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  72aaf1b

Commits on Mar 17, 2017

• Added empirical protein model stmtREV of Li et al 2014

  cymon

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  74893a1

• Missing comma

  cymon

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  79b2b19

• Merge branch 'master' into cymon-working

  cymon

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  f71214f

• Merge branch 'master' of https://github.com/cymon/p4-phylogenetics into cymon-working

  cymon

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  71ff540

Commits on Mar 20, 2017

• Typo: really should test these things before committing...

  cymon

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  fb5b715

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

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  ba31dde

Commits on May 3, 2017

• Handle aa ambiguities in Dayhoff recoding

  cymon

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  2d17c43

Commits on May 5, 2017

• Resolved merge conflict by ingnoring upstream.

  cymon

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  6d9b47b

Commits on Jun 7, 2017

• Resolved merge conflict by ingnoring upstream.

  cymon

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  b382b60

• Merge branch 'master' into cymon-working

  cymon

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  6ea768b

Commits on Aug 30, 2017

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

  cymon

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  398caab

Commits on Oct 18, 2017

• Merge branch 'master' into cymon-working

  cymon

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  2fab389

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

  cymon

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  f089868

Commits on Dec 11, 2017

• Added option to start recoding protein data into group starting with the zero

  Show description for d1299c2
  cymon

  committed
  d1299c2

Commits on Dec 12, 2017

• Cleaned up getMinmaxChiSqGroups() - it might actually work now...

  cymon

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  a0e538b

• Allow Dayhoff recoding by numbers to start with 0

  cymon

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  329a62e

Commits on Jan 29, 2018

• Merge branch 'master' into cymon-working

  cymon

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  a9889e9

Commits on Feb 1, 2018

• Merge branch 'master' into cymon-working

  Show description for eaefe23
  cymon

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  eaefe23

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

  Show description for 569baf1
  cymon

  committed
  569baf1

Commits on Feb 2, 2018

• Expanation of path modification in p4 start script

  cymon

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  aa0f4f0

Commits on Feb 19, 2018

• Merge branch 'master' into cymon-working

  cymon

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  82bde71

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

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  311cd1a

Commits on Mar 23, 2018

• Calculate tree heights (lead to root cumulative br lens)

  cymon

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  83981d1

• Merge branch 'master' into cymon-working

  cymon

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  bd6fc70

Commits on Apr 10, 2018

• Merge branch 'master' into cymon-working

  cymon

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  8168e1d

Commits on Apr 11, 2018

• Merge branch 'master' into cymon-working

  cymon

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  d7acf86

• Build both python2 and python3 pf binaries

  cymon

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  52b0180

Commits on Apr 23, 2018

• Merge branch 'master' into cymon-working

  cymon

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  c0c1d10

Commits on May 3, 2018

• Merge branch 'master' into cymon-working

  cymon

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  c973cdc

Commits on Aug 31, 2018

• Resolved merge conflict on make_pf.sh

  cymon

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  7b3e1f2

Commits on Nov 22, 2018

• Added warning to guessing dna/aa's with Phylip format

  cymon

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  2af6015

• Merge branch 'master' into cymon-working

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  2b8725d

Commits on Mar 25, 2019

• Merge branch 'master' into cymon-working

  cymon

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  0ed07fa

• Change default python from 2 to 3

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  993b719

• Added protien models prasREV and gnetREV for Li and Filipe

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  01b6de7

• Merge branch 'new-models' into cymon-working

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  2fe6648

Commits on Mar 29, 2019

• Added greater precision for the values in gnetREV and prasREV

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  52ae60b

Commits on Apr 1, 2019

• Defaulting to python3

  

  Cymon J. Cox

  committed
  e17b6fc

Commits on May 15, 2019

• io.Bytes to io.String in treefilelite.py and added /usr/local/lib64 to setup.py

  Show description for 53b52a7
  cymon

  committed
  53b52a7

Commits on May 21, 2019

• Merge branch 'master' into cymon-working

  cymon

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  137d128

• Fixed BytesI0/StringIO issues in treefilelite.py

  cymon

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  35fc9e1

Commits on Jul 26, 2019

• Merge branch 'master' into cymon-working

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  dac236f

Commits on Sep 13, 2019

• Merge branch 'master' into cymon-working

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  2616241

• Configuration for Ceta. Check that git is installed before call it.

  cymon

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  35d4cdb

Commits on Oct 28, 2019

• Resolved merge conflicts with upstream.

  cymon

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  32d6df4

• Resolved merge conflicts with upstream.

  cymon

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  2bf4408

• Removed old ref to binary

  cymon

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  2085ffe

Commits on Nov 12, 2019

• Resolved merge conflict by ingnoring upstream.

  cymon

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  152636d

• Added paths for weird include places on ceta

  cymon

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  6b6afa9

• Merge branch 'cymon-working' of https://github.com/cymon/p4-phylogenetics into cymon-working

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  e04a24c

Commits on Nov 18, 2019

• Merge branch 'master' into cymon-working

  cymon

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  16fc201

Commits on Nov 28, 2019

• Merge branch 'master' into cymon-working

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  7cb08a4

Commits on Nov 29, 2019

• Added a 'stop' sample parameter to pnumbers.Numbers

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  a86d1ab

Commits on Dec 19, 2019

• Merge branch 'master' into cymon-working

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  dc95c23

Commits on Jan 6, 2020

• Merge branch 'master' into cymon-working

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  04c29eb

Commits on Jan 30, 2020

• Merge branch 'master' into cymon-working

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  0c8b535

Commits on Feb 18, 2020

• Merge branch 'master' into cymon-working

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  f0835f0

Commits on Mar 4, 2020

• Merge branch 'master' into cymon-working

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  87d7f46

Commits on Mar 5, 2020

• Merge branch 'master' into cymon-working

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  2a51726

Commits on Mar 12, 2020

• Merge branch 'master' into cymon-working

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  a54c906

Commits on Apr 19, 2020

• Merge branch 'master' into cymon-working

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  4e1781b

Commits on Sep 9, 2020

• Merge branch 'master' into cymon-working

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  44d48f8

Commits on Sep 10, 2020

• Merge branch 'master' into cymon-working

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  e03175f

• Reverting func.py to master

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  038264c

Commits on Mar 12, 2021

• Merge branch 'master' into cymon-working

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  d7bc881

Commits on Jan 7, 2022

• Merge branch 'master' into cymon-working

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  07ba7b0

Commits on Feb 15, 2022

• Merge branch 'master' into cymon-working

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  7a0553f

Commits on Apr 18, 2022

• Merge branch 'master' into cymon-working

  cymon

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  d8b7d48

Commits on Apr 21, 2022

• Resolved merge conflict by being confused.

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  688f163

Commits on Jul 4, 2022

• Merge branch 'master' into cymon-working

  cymon

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  ff958f2

• Manual removed a left over >>>>HEAD

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  950af23

• Removed >>>>HEAD after failed merge

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  7f2ffc6