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base fork: michaelbarton/fluorescens-manuscript-figures
base: 210a28d1f3
...
head fork: michaelbarton/fluorescens-manuscript-figures
compare: 74763d293f
Checking mergeability… Don't worry, you can still create the pull request.
Commits on Apr 15, 2011
@michaelbarton Write sequences as fasta to tmp dir 50a81b1
@michaelbarton Auto scaffold genome 6cb3032
@michaelbarton Generate genome alignments 089c5b7
@michaelbarton Plot genome rearrangments c464d29
@michaelbarton Plot alignments along x-axis of chart 2c2eeaf
@michaelbarton Swith x and y axis 169ba9e
@michaelbarton Merge branch 'rearrangement' into develop 4fa94e9
Commits on Apr 18, 2011
@michaelbarton Create gene database based on numbers 929b304
@michaelbarton Find orthlogs using phmmer 6fcc1c5
@michaelbarton Reorganise rake tasks ba7284c
@michaelbarton Parse hmmer output 641dcbc
@michaelbarton Cluster hmmer data c94612b
@michaelbarton Copy ortholog data over 0a897ed
Commits on Apr 19, 2011
@michaelbarton Add R124 genes to ortholog analysis fd22e7b
Commits on Apr 20, 2011
@michaelbarton Estimate ortholog clusters 8fb6200
Commits on Jul 14, 2011
@michaelbarton Update to latest version of genome build 613919e
@michaelbarton Update alignment plot for new genome build f559030
@michaelbarton Re-organise rakefile into namespaces 9528284
@michaelbarton Rake task to generate genome size data 11a0432
Commits on Jul 18, 2011
@michaelbarton Add strain to genome size data ec97daf
@michaelbarton Recalculate genome size data with gene count b04ca7f
@michaelbarton Replot genome size vs gene count 15671f4
Commits on Jul 19, 2011
@michaelbarton Rake namespace for creating all plots e9c7b22
@michaelbarton Add median gene density to genome size plot 7301f9d
@michaelbarton Merge branch 'develop' into orthologs
Conflicts:
	Rakefile
19cf634
@michaelbarton Update database and core number for ortholog search 6084645
Commits on Jul 20, 2011
@michaelbarton Fix clustering rake tasks f2898b6
@michaelbarton Update legends for genome dotplot 0c53a1a
@michaelbarton Add non-matching genes to clusters f0d1244
@michaelbarton Calculate species in each cluster f07edc8
@michaelbarton Merge branch 'orthologs' into develop 2e311cc
Commits on Jul 25, 2011
@michaelbarton Switch repository for reference genomes 3b470c6
Commits on Sep 06, 2011
@michaelbarton Update to latest version of R124 assembly 6b59a45
@michaelbarton Fix rake task for generating synteny data 2c2cb28
Commits on Mar 06, 2012
@michaelbarton Fix pf0-1 in figure legend e909151
@michaelbarton Add figure keys to image 4b3ffd2
Commits on Mar 08, 2012
@michaelbarton Generate postscript output 52fee43
@michaelbarton Print postscript for gene plot c2a9f52
Commits on Apr 02, 2013
@michaelbarton Fetch genome sequences from S3
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
8653dcb
@michaelbarton Count genome length and number of genes
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
4929a62
@michaelbarton Plot gene density figure
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
32c46c2
Commits on Apr 03, 2013
@michaelbarton Fix script for counting density
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
9f16028
@michaelbarton Generate fasta files of genomes
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
4d36f29
@michaelbarton Generate synteny coordinates
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
6712859
@michaelbarton Regenerate genome dotplot
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
5e9a0c4
@michaelbarton Add code for generating growth rate figure
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
103eeb7
@michaelbarton Reorganise plotting scripts
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
4dbe574
@michaelbarton Reset repository
Signed-off-by: Michael Barton <mail@michaelbarton.me.uk>
389a322
@michaelbarton Merge branch 'fix' into develop e921b4d
@michaelbarton Merge branch 'develop' 74763d2
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