Overview - Effects of cost in protein evolution

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Added validation to site mutation to ... was committed by Michael Barton
Monday Sep 08

Commit [6eeef96c5342136007e86022fa8af2c81964595f]
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Added alignment codon fixtures http:/... was committed by Michael Barton 01:47 PM
Commit [e15e34508b5c03d9d8f4832806226aabf3f5fa2d]
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Added new specs for testing site muta... was committed by Michael Barton 01:47 PM
Commit [e61c87f0b698e857554a079de5f1f5421aa60d3e]
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Added factory for site mutation http:... was committed by Michael Barton 01:47 PM
Commit [e6c9c7a49cdf0dfd2ef5a01273a3f3f235bafa8e]
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Updated evolutionary rate specing to ... was committed by Michael Barton 01:47 PM
Commit [fc788bc9c659b9b0d7f7ceaaa4d89d8b18110658]
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Added specing to test that wrong orde... was committed by Michael Barton 01:46 PM
Commit [04d98e1a089cb21718a828659200ea75fec6bba5]
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Alignment Codons are created before a... was committed by Michael Barton 01:46 PM
Commit [4802b30b77755444b81498989cb3cf417933d49d]
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Added specing to ensure that each ali... was committed by Michael Barton 01:46 PM
Commit [6d6118781b57247742abaee3a5bfddd925216e00]
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Updated alignment codon spec to use f... was committed by Michael Barton 01:46 PM
Commit [3aee233c2cf51d690259dd02975528d94f2c0666]
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Factories loaded in spec helper http:... was committed by Michael Barton 01:46 PM
Commit [41dc2b2fabf3ed210ba3d1c573244198f51da291]
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Created factory for alignment codon h... was committed by Michael Barton 01:45 PM
Commit [5da7173a296af8a1d5fcfd19154a6bde75f29f9b]
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Updated alignment codon specing to us... was committed by Michael Barton 01:45 PM
Commit [672e6f9e51e539f26a0f63e90f34e995eb0067c8]
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Corrected indentation http://github.c... was committed by Michael Barton 01:45 PM
Commit [5fb537a3e7be49591c8eff3d3e2a4fe56afb8fc6]
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Added fixture files for gene and alig... was committed by Michael Barton 01:45 PM
Commit [3db85083feb92f15d4c77af2c910dcadff31d106]
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Added a load fixtures method spec hel... was committed by Michael Barton 01:45 PM
Commit [ffa36e046f35dea5afa3da432618570d0b1c98b1]
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Merge branch 'master' into fixtures h... was committed by Michael Barton 01:45 PM
Commit [606cd9839d93b027f38108147718b6cf39d1f034]
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Updated gene specing, load_gene is no... was committed by Michael Barton 01:45 PM
Commit [f819c153d02548855d6505748e2b2ab9859f1c81]
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Converted alignment spec to use fixtu... was committed by Michael Barton 01:44 PM
Commit [bef284df1b44dcfecf8be35fed2db498a2f65b57]
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Created rake task to execute starfish... was committed by Michael Barton
Thursday Sep 04

Commit [a42c50355f3dc855fd261ced8acb653ef3177f87]
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Added starfish class to execute RindR... was committed by Michael Barton 01:55 PM
Commit [4fc0d25f274b131dd2067efe668a71fee49aa718]
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Added helper method to rind runner to... was committed by Michael Barton 01:54 PM
Commit [fec318251cf33aab5b7677e82f11a7648bcf103c]
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Added method to populate amino acid f... was committed by Michael Barton 01:26 PM
Commit [24733395c808975199d6931df309b7fce6dc692f]
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Added specing for amino acid frequenc... was committed by Michael Barton 01:25 PM
Commit [41f30c7c80aa82489371a2d0632b4b40d9f2032b]
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Added indicies to amino acid frequenc... was committed by Michael Barton 01:24 PM
Commit [a9dffd406c4773be36329d2da8f8dcfea15846fc]
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Fixed amino acid class http://github.... was committed by Michael Barton 01:24 PM
Commit [c8db0c2b17364d6ee36dc7b22f09cc0a6db0484d]
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Removed erroneous print statements ht... was committed by Michael Barton
Wednesday Sep 03

Commit [41e827e4f686f89871d89980b8f5805e8ae61501]
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Created rind runner helper http://git... was committed by Michael Barton 06:23 PM
Commit [138e3e6daa46ac9ffddc2e3aa7b347462ced5848]
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Added specing for running rind inside... was committed by Michael Barton 06:22 PM
Commit [65566be0abf109f33a05f16c919089dd2d58b01e]
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Fixed spacing in migration http://git... was committed by Michael Barton 06:22 PM
Commit [07bf83feab1a35cc104b948caae4900161655a73]
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Merge branch 'master' into rind http:... was committed by Michael Barton 06:22 PM
Commit [a8caa720c9c7240c29407543589daee6a3628f3d]
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Added active record fixtures to load ... was committed by Michael Barton 06:21 PM
Commit [876d8c4f977c6a555cee22f387da3b30bc69ab87]
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Added helper method to evolutionary r... was committed by Michael Barton 06:21 PM
Commit [a2fe5b5a9d778ea312fe30ee0b801915f8635a46]
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Added model and migration for amino a... was committed by Michael Barton 06:20 PM
Commit [2107ac64ea1bb0a1165e7ca06db41b36dc4d9a13]
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Added code to load amino acid data ht... was committed by Michael Barton 06:20 PM
Commit [27a4d7f01a2484bcec3c768507614b45c9a5ee89]
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Created model and migration for amino... was committed by Michael Barton 06:20 PM
Commit [d8f7f22cfe138c9a13d9a6a74ea5e590aa810888]
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Updated evolutionary rate estimation ... was committed by Michael Barton
Monday Sep 01

Commit [0ed2170d5d5795bdd1c053481d06ea10c2b45083]
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Updated specing for adding unrooted t... was committed by Michael Barton 04:16 PM
Commit [60e80449ea071ca2fe512b59af9d9fde9fb326d8]
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Updated alignment to return an unroot... was committed by Michael Barton 04:16 PM
Commit [db10dd6265063364d292f01e1a5a34fcae50af74]
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Added method in evolutionary rate to ... was committed by Michael Barton 04:15 PM
Commit [4852cefae25bbe2a6e5f4287847e0c72c7e7253c]
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Added column in gene mutations table ... was committed by Michael Barton 04:15 PM
Commit [6b1cebd45208e0f8f0be5595e0c63ddb69910b89]
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Added new version of bioruby http://g... was committed by Michael Barton 04:15 PM
Commit [a22450610a0f33a9be1d96ca07a8a4ec0e79342f]
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Correlate tree length with non-synonymous mutations was updated by Michael Barton
Tuesday Aug 26

#15 / Estimate sitewise evolution rates / new
ticket
Estimate time spent in each amino acid was created by Michael Barton 10:13 AM
#16 / Calculate cost for alignment column / new
ticket
Calculate cost for alignment column was created by Michael Barton 10:12 AM
1 ticket open, 1 total
milestone
Correlate tree length with non-synony... was created by Michael Barton 10:11 AM
#15 / Estimate sitewise evolution rates / new
ticket
Added tasks for loading and clearing ... was committed by Michael Barton
Thursday Aug 21

Commit [45f50f60dc1e55501b370707ca00170a5bdb6c92]
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Updated tasks for clearing site and g... was committed by Michael Barton 05:55 PM
Commit [a7730d75b7d34f03db0c792b9639c27fa24df7fc]
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Updated loading of gene wise mutation... was committed by Michael Barton 05:55 PM
Commit [fdbb4b28d623992ccf08746fa4fe5d9d13696b10]
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Updated table columns names for gene ... was committed by Michael Barton 05:55 PM
Commit [1141f1153c9ee34b4b8e1bb6352c05bebb0abcf0]
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Added fastercsv gem to environment ht... was committed by Michael Barton 05:55 PM
Commit [4758f8bbb3b0205fb2238cfa29428843e448994b]
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Michaelbarton Effects of cost in protein evolution

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