synmut.git
6 years agoreformat for JVI publication
Richard [Thu, 6 Jun 2013 16:07:20 +0000 (18:07 +0200)]
reformat for JVI

6 years agosubmission to JVI
Richard [Thu, 6 Jun 2013 13:01:15 +0000 (15:01 +0200)]
submission to JVI

6 years agoa few more little changes
Fabio Zanini [Thu, 6 Jun 2013 09:55:09 +0000 (11:55 +0200)]
a few more little changes

6 years agointro: dumped nonsyn and shrunk codon usage
Fabio Zanini [Thu, 6 Jun 2013 09:45:20 +0000 (11:45 +0200)]
intro: dumped nonsyn and shrunk codon usage

6 years agoText changes + fig 3A for color blind
Fabio Zanini [Thu, 6 Jun 2013 08:57:36 +0000 (10:57 +0200)]
Text changes + fig 3A for color blind

6 years agomore little changes
Fabio Zanini [Wed, 5 Jun 2013 17:00:37 +0000 (19:00 +0200)]
more little changes

6 years agoMerge branch 'temp' into new_submission: scripts.
Fabio Zanini [Wed, 5 Jun 2013 16:45:29 +0000 (18:45 +0200)]
Merge branch 'temp' into new_submission: scripts.

6 years agolittle changes in discussion
Fabio Zanini [Wed, 5 Jun 2013 16:45:21 +0000 (18:45 +0200)]
little changes in discussion

6 years agofixed typos
Richard [Wed, 5 Jun 2013 15:00:57 +0000 (17:00 +0200)]
fixed typos

6 years agolittle changes
Richard [Wed, 5 Jun 2013 14:53:35 +0000 (16:53 +0200)]
little changes

6 years agoMore on the same
Fabio Zanini [Wed, 5 Jun 2013 14:40:25 +0000 (16:40 +0200)]
More on the same

6 years agoModified fixation_times script to include nonsynonymous
Fabio Zanini [Wed, 5 Jun 2013 13:40:35 +0000 (15:40 +0200)]
Modified fixation_times script to include nonsynonymous

6 years agostreamlining discussion
Richard [Wed, 5 Jun 2013 09:59:24 +0000 (11:59 +0200)]
streamlining discussion

6 years agochanges, mostly in discussion
Richard [Tue, 4 Jun 2013 16:57:29 +0000 (18:57 +0200)]
changes, mostly in discussion

6 years agoImplemented Richard's suggestions (including 'mutation' -> SNV)
Fabio Zanini [Fri, 31 May 2013 13:08:19 +0000 (15:08 +0200)]
Implemented Richard's suggestions (including 'mutation' -> SNV)

6 years agoMore discussion on RNA stuff + citations
Fabio Zanini [Wed, 29 May 2013 09:42:10 +0000 (11:42 +0200)]
More discussion on RNA stuff + citations

6 years agoTest changes, still not done with cites
Fabio Zanini [Sun, 26 May 2013 15:08:25 +0000 (17:08 +0200)]
Test changes, still not done with cites

6 years agoSome aesthetic stuff from Richard which I had forgotten
Fabio Zanini [Fri, 17 May 2013 10:23:44 +0000 (12:23 +0200)]
Some aesthetic stuff from Richard which I had forgotten

6 years agoFigure labels size, little text
Fabio Zanini [Fri, 17 May 2013 10:04:30 +0000 (12:04 +0200)]
Figure labels size, little text

6 years agoSmall changes in text
Fabio Zanini [Fri, 17 May 2013 09:02:24 +0000 (11:02 +0200)]
Small changes in text

6 years agoOld text
Fabio Zanini [Fri, 17 May 2013 08:54:25 +0000 (10:54 +0200)]
Old text

6 years agoAuthor summary
Fabio Zanini [Tue, 12 Mar 2013 13:51:20 +0000 (14:51 +0100)]
Author summary

6 years agoremove packages disliked by plos
Fabio Zanini [Tue, 12 Mar 2013 13:09:11 +0000 (14:09 +0100)]
remove packages disliked by plos

6 years agoFormat for PLoS CompBio: missing author summary
Fabio Zanini [Tue, 12 Mar 2013 11:39:18 +0000 (12:39 +0100)]
Format for PLoS CompBio: missing author summary

6 years agosmall fig changes
Fabio Zanini [Tue, 12 Mar 2013 08:44:37 +0000 (09:44 +0100)]
small fig changes

6 years agoMerge branch 'publication' (small typo)
Fabio Zanini [Tue, 12 Mar 2013 08:40:16 +0000 (09:40 +0100)]
Merge branch 'publication' (small typo)

Conflicts:
synmut.tex

6 years agoacknowledgment typo
Richard Neher [Mon, 4 Mar 2013 16:27:09 +0000 (17:27 +0100)]
acknowledgment typo

6 years agopublic
Richard Neher [Mon, 4 Mar 2013 15:31:29 +0000 (16:31 +0100)]
public

6 years agono hyperref
Richard Neher [Mon, 4 Mar 2013 15:22:09 +0000 (16:22 +0100)]
no hyperref

6 years agofixed typos, thanks Taylor
Richard Neher [Mon, 4 Mar 2013 14:38:09 +0000 (15:38 +0100)]
fixed typos, thanks Taylor

6 years agoLittle changes here and there
Fabio Zanini [Fri, 1 Mar 2013 17:11:20 +0000 (18:11 +0100)]
Little changes here and there

6 years agosupplementary figures correct numbering
Fabio Zanini [Fri, 1 Mar 2013 16:14:09 +0000 (17:14 +0100)]
supplementary figures correct numbering

6 years agolittle edits here and there, moved supplement body into separate file such that we...
Richard Neher [Fri, 1 Mar 2013 13:18:59 +0000 (14:18 +0100)]
little edits here and there, moved supplement body into separate file such that we can include it into the main text as an appendix for submission

6 years agofig2a little aesthetics
Fabio Zanini [Thu, 28 Feb 2013 19:45:21 +0000 (16:45 -0300)]
fig2a little aesthetics

6 years agoredid Fig 2a, adjusted text
Richard Neher [Thu, 28 Feb 2013 09:36:09 +0000 (10:36 +0100)]
redid Fig 2a, adjusted text

6 years agotypo
Fabio Zanini [Tue, 26 Feb 2013 18:33:43 +0000 (19:33 +0100)]
typo

6 years agoFigures'labels.
Fabio Zanini [Tue, 26 Feb 2013 18:27:00 +0000 (19:27 +0100)]
Figures'labels.

6 years agoincorporated Pleuni's and Jan's comments, still need to do smth about the interpretat...
Richard Neher [Tue, 26 Feb 2013 18:09:14 +0000 (19:09 +0100)]
incorporated Pleuni's and Jan's comments, still need to do smth about the interpretation/nonsyn deleterious hitchhikers

6 years agoJan suggestions (fig labels)
Fabio Zanini [Tue, 26 Feb 2013 16:26:51 +0000 (17:26 +0100)]
Jan suggestions (fig labels)

6 years agoword version for Jan
Fabio Zanini [Fri, 15 Feb 2013 09:51:10 +0000 (10:51 +0100)]
word version for Jan

6 years agotypes and edits in figure captions
richard [Wed, 13 Feb 2013 17:55:06 +0000 (18:55 +0100)]
types and edits in figure captions

6 years agotext small changes
Fabio Zanini [Wed, 13 Feb 2013 09:38:26 +0000 (10:38 +0100)]
text small changes

6 years agoFig.1 has p10; Fig S3 -> S3/S4; more details on epitopes; S2 larger
Fabio Zanini [Tue, 12 Feb 2013 17:20:20 +0000 (18:20 +0100)]
Fig.1 has p10; Fig S3 -> S3/S4; more details on epitopes; S2 larger

6 years agoedits throughout, reorganized discussion and supplement
richard [Tue, 12 Feb 2013 14:31:43 +0000 (15:31 +0100)]
edits throughout, reorganized discussion and supplement

6 years agodiscussion reshuffled
Fabio Zanini [Mon, 11 Feb 2013 14:54:47 +0000 (15:54 +0100)]
discussion reshuffled

6 years agonew Fig 4B plus some editing
Fabio Zanini [Mon, 11 Feb 2013 10:58:23 +0000 (11:58 +0100)]
new Fig 4B plus some editing

6 years agosupplement only captions, more details about simulations. need to redo simulations...
Fabio Zanini [Sun, 10 Feb 2013 11:25:10 +0000 (12:25 +0100)]
supplement only captions, more details about simulations. need to redo simulations without complex epitopes for 4B

6 years agoEdits in main text and supplement. Supplement needs more work. Methods
richard [Sat, 9 Feb 2013 16:28:31 +0000 (17:28 +0100)]
Edits in main text and supplement. Supplement needs more work. Methods
need to be somewhat more detailed.

6 years agoSHAPE files plus simulation script
Fabio Zanini [Wed, 6 Feb 2013 10:29:01 +0000 (11:29 +0100)]
SHAPE files plus simulation script

6 years agosmall change in the methods
Fabio Zanini [Mon, 4 Feb 2013 18:24:44 +0000 (19:24 +0100)]
small change in the methods

6 years agolifted remote external dependencies (should be self-contained now)
Fabio Zanini [Mon, 4 Feb 2013 18:12:56 +0000 (19:12 +0100)]
lifted remote external dependencies (should be self-contained now)

6 years agoalignments added
Fabio Zanini [Mon, 4 Feb 2013 17:40:45 +0000 (18:40 +0100)]
alignments added

6 years agoscripts for supplementary
Fabio Zanini [Mon, 4 Feb 2013 14:28:07 +0000 (15:28 +0100)]
scripts for supplementary

6 years agosimulation scripts
Fabio Zanini [Mon, 4 Feb 2013 13:49:00 +0000 (14:49 +0100)]
simulation scripts

6 years agoPCA of good patient in suppl
Fabio Zanini [Mon, 4 Feb 2013 11:05:06 +0000 (12:05 +0100)]
PCA of good patient in suppl

6 years agoall experimental scripts (but no alignments yet, nor remote modules)
Fabio Zanini [Mon, 4 Feb 2013 10:47:13 +0000 (11:47 +0100)]
all experimental scripts (but no alignments yet, nor remote modules)

6 years agoadded first scripts
Fabio Zanini [Sun, 3 Feb 2013 17:43:28 +0000 (18:43 +0100)]
added first scripts

6 years agofig.1 refers to p1
Fabio Zanini [Sun, 3 Feb 2013 17:42:48 +0000 (18:42 +0100)]
fig.1 refers to p1

6 years agotext small changes
Fabio Zanini [Sun, 3 Feb 2013 12:21:40 +0000 (13:21 +0100)]
text small changes

6 years agosupplementary first draft
Fabio Zanini [Fri, 1 Feb 2013 16:14:14 +0000 (17:14 +0100)]
supplementary first draft

6 years agoadded 2nd rev exon to conservation plot
Fabio Zanini [Wed, 30 Jan 2013 17:38:34 +0000 (18:38 +0100)]
added 2nd rev exon to conservation plot

6 years agorewrote discussion and abstract
Richard [Wed, 30 Jan 2013 10:21:10 +0000 (11:21 +0100)]
rewrote discussion and abstract

6 years agocorrected time-dep sims and figure adaptations
Fabio Zanini [Tue, 29 Jan 2013 16:45:37 +0000 (17:45 +0100)]
corrected time-dep sims and figure adaptations

6 years agoMerge remote-tracking branch 'inn/master'
Fabio Zanini [Tue, 29 Jan 2013 15:40:51 +0000 (16:40 +0100)]
Merge remote-tracking branch 'inn/master'

6 years agoexemplary figure on both complex epitopes and time-dep selection
Fabio Zanini [Tue, 29 Jan 2013 15:40:43 +0000 (16:40 +0100)]
exemplary figure on both complex epitopes and time-dep selection

6 years agoMerge branch 'master' of inn.eb.local:/ebio/ag-neher/share/our_papers/synmut
Richard [Tue, 29 Jan 2013 14:40:14 +0000 (15:40 +0100)]
Merge branch 'master' of inn.eb.local:/ebio/ag-neher/share/our_papers/synmut

6 years agoedits in captions
Richard [Tue, 29 Jan 2013 14:39:14 +0000 (15:39 +0100)]
edits in captions

6 years agoSimulations both gating (syn and nonsyn)
Fabio Zanini [Tue, 29 Jan 2013 14:25:54 +0000 (15:25 +0100)]
Simulations both gating (syn and nonsyn)

6 years agoMerge remote-tracking branch 'inn/master'
Fabio Zanini [Tue, 29 Jan 2013 14:17:07 +0000 (15:17 +0100)]
Merge remote-tracking branch 'inn/master'

6 years agofig 2B without rev/tat second exon
Fabio Zanini [Tue, 29 Jan 2013 14:16:51 +0000 (15:16 +0100)]
fig 2B without rev/tat second exon

6 years agoMerge branch 'master' of inn.eb.local:/ebio/ag-neher/share/our_papers/synmut
Richard [Mon, 28 Jan 2013 17:35:26 +0000 (18:35 +0100)]
Merge branch 'master' of inn.eb.local:/ebio/ag-neher/share/our_papers/synmut

6 years agocombed through the text. Discussion and captions still need work
Richard [Mon, 28 Jan 2013 17:33:57 +0000 (18:33 +0100)]
combed through the text. Discussion and captions still need work

6 years agohistograms for SHAPE instead of cumulative
Fabio Zanini [Mon, 28 Jan 2013 17:25:41 +0000 (18:25 +0100)]
histograms for SHAPE instead of cumulative

6 years agomerged conflict, take care of figure captions
Richard [Mon, 28 Jan 2013 10:30:32 +0000 (11:30 +0100)]
merged conflict, take care of figure captions

6 years agoMerge branch 'master' of inn.eb.local:/ebio/ag-neher/home/fzanini/phd/papers/synmut
Richard [Mon, 28 Jan 2013 10:22:32 +0000 (11:22 +0100)]
Merge branch 'master' of inn.eb.local:/ebio/ag-neher/home/fzanini/phd/papers/synmut

6 years agomy changes
Richard [Mon, 28 Jan 2013 10:22:26 +0000 (11:22 +0100)]
my changes

6 years agotext revisited around new figure
Fabio Zanini [Mon, 28 Jan 2013 10:18:31 +0000 (11:18 +0100)]
text revisited around new figure

6 years agonew figure from simulations, broader
Fabio Zanini [Mon, 28 Jan 2013 09:49:32 +0000 (10:49 +0100)]
new figure from simulations, broader

6 years agoAdded bootstrap on Pfix
Fabio Zanini [Fri, 25 Jan 2013 14:40:11 +0000 (15:40 +0100)]
Added bootstrap on Pfix

6 years agofigures adapted
Fabio Zanini [Thu, 24 Jan 2013 16:37:14 +0000 (17:37 +0100)]
figures adapted

6 years agomerged conflicts
Richard [Wed, 23 Jan 2013 16:17:35 +0000 (17:17 +0100)]
merged conflicts

6 years agoText adapted to new figures
Fabio Zanini [Wed, 23 Jan 2013 13:18:25 +0000 (14:18 +0100)]
Text adapted to new figures

6 years agonew figures from simulations
Fabio Zanini [Tue, 22 Jan 2013 19:21:06 +0000 (20:21 +0100)]
new figures from simulations

7 years agoedits throughout, added a few references
Richard [Fri, 4 Jan 2013 17:24:32 +0000 (18:24 +0100)]
edits throughout, added a few references

7 years agomerge few details
Fabio Zanini [Wed, 2 Jan 2013 11:12:37 +0000 (12:12 +0100)]
merge few details

7 years agoMerge remote-tracking branch 'richard/master'
Fabio Zanini [Wed, 2 Jan 2013 11:01:59 +0000 (12:01 +0100)]
Merge remote-tracking branch 'richard/master'

7 years agofigures updates
Fabio Zanini [Wed, 2 Jan 2013 11:00:38 +0000 (12:00 +0100)]
figures updates

7 years agodon't know exactly
Richard [Fri, 28 Dec 2012 10:28:13 +0000 (11:28 +0100)]
don't know exactly

7 years agoresolved conflict
Richard [Sun, 23 Dec 2012 03:34:32 +0000 (04:34 +0100)]
resolved conflict

7 years agominor edits
Richard [Sun, 23 Dec 2012 03:27:10 +0000 (04:27 +0100)]
minor edits

7 years agosmall changes here and there
Fabio Zanini [Fri, 21 Dec 2012 22:21:09 +0000 (14:21 -0800)]
small changes here and there

7 years agoMethods
Fabio Zanini [Thu, 20 Dec 2012 20:01:37 +0000 (12:01 -0800)]
Methods

7 years agoreview, more supplementary figures
Fabio Zanini [Sat, 15 Dec 2012 02:38:11 +0000 (18:38 -0800)]
review, more supplementary figures

7 years agoSynonymous conservation
Fabio Zanini [Wed, 12 Dec 2012 03:12:54 +0000 (19:12 -0800)]
Synonymous conservation

7 years agosome changes applied
Fabio Zanini [Sat, 8 Dec 2012 07:35:57 +0000 (23:35 -0800)]
some changes applied

7 years agomajor rearrangements, rewriting -> first draft from RAN, needs fleshing out, new...
Richard [Thu, 6 Dec 2012 06:12:13 +0000 (07:12 +0100)]
major rearrangements, rewriting -> first draft from RAN, needs fleshing out, new figures etc

7 years agomajor rearrangements, rewriting -> first draft from RAN, needs fleshing out, new...
Richard [Thu, 6 Dec 2012 06:09:42 +0000 (07:09 +0100)]
major rearrangements, rewriting -> first draft from RAN, needs fleshing out, new figures etc

7 years agoCoalescent tree + C2-V5
Fabio Zanini [Tue, 4 Dec 2012 01:43:35 +0000 (17:43 -0800)]
Coalescent tree + C2-V5

7 years agotypo + caption package
Fabio Zanini [Mon, 3 Dec 2012 18:44:00 +0000 (10:44 -0800)]
typo + caption package

7 years agodraft0
Fabio Zanini [Sun, 2 Dec 2012 02:00:19 +0000 (18:00 -0800)]
draft0